Crispr-based genome modification and regulation

ABSTRACT

The present invention provides RNA-guided endonucleases, which are engineered for expression in eukaryotic cells or embryos, and methods of using the RNA-guided endonuclease for targeted genome modification in eukaryotic cells or embryos. Also provided are fusion proteins, wherein each fusion protein comprises a CRISPR/Cas-like protein or fragment thereof and an effector domain. The effector domain can be a cleavage domain, an epigenetic modification domain, a transcriptional activation domain, or a transcriptional repressor domain. Also provided are methods for using the fusion proteins to modify a chromosomal sequence or regulate expression of a chromosomal sequence.

FIELD OF THE INVENTION

The present disclosure relates targeted genome modification. Inparticular, the disclosure relates to RNA-guided endonucleases or fusionproteins comprising CRISPR/Cas-like protein and methods of using saidproteins to modify or regulate targeted chromosomal sequences.

BACKGROUND OF THE INVENTION

Targeted genome modification is a powerful tool for genetic manipulationof eukaryotic cells, embryos, and animals. For example, exogenoussequences can be integrated at targeted genomic locations and/orspecific endogenous chromosomal sequences can be deleted, inactivated,or modified. Current methods rely on the use of engineered nucleaseenzymes, such as, for example, zinc finger nucleases (ZFNs) ortranscription activator-like effector nucleases (TALENs). These chimericnucleases contain programmable, sequence-specific DNA-binding moduleslinked to a nonspecific DNA cleavage domain. Each new genomic target,however, requires the design of a new ZFN or TALEN comprising a novelsequence-specific DNA-binding module. Thus, these custom designednucleases tend to be costly and time-consuming to prepare. Moreover, thespecificities of ZFNs and TALENS are such that they can mediateoff-target cleavages.

Thus, there is a need for a targeted genome modification technology thatdoes not require the design of a new nuclease for each new targetedgenomic location. Additionally, there is a need for a technology withincreased specificity with few or no off-target effects.

SUMMARY OF THE INVENTION

Among the various aspects of the present disclosure is the provision ofan isolated RNA-guided endonuclease, wherein the endonuclease comprisesat least one nuclear localization signal, at least one nuclease domain,and at least one domain that interacts with a guide RNA to target theendonuclease to a specific nucleotide sequence for cleavage. In oneembodiment, the endonuclease can be derived from a Cas9 protein. Inanother embodiment, the endonuclease can be modified to lack at leastone functional nuclease domain. In other embodiments, the endonucleasecan further comprise a cell-penetrating domain, a marker domain, orboth. In a further embodiment, the endonuclease can be part of aprotein-RNA complex comprising the guide RNA. In some instances, theguide RNA can be a single molecule comprising a 5′ region that iscomplementary to a target site. Also provided is an isolated nucleicacid encoding any of the RNA-guided endonucleases disclosed herein. Insome embodiments, the nucleic acid can be codon optimized fortranslation in mammalian cells, such as, for example, human cells. Inother embodiments, the nucleic acid sequence encoding the RNA-guidedendonuclease can be operably linked to a promoter control sequence, andoptionally, can be part of a vector. In other embodiments, a vectorcomprising sequence encoding the RNA-guided endonuclease, which can beoperably linked to a promoter control sequence, can also comprisesequence encoding a guide RNA, which can be operably linked to apromoter control sequence.

Another aspect of the present invention encompasses a method formodifying a chromosomal sequence in a eukaryotic cell or embryo. Themethod comprises introducing into a eukaryotic cell or embryo (i) atleast one RNA-guided endonuclease comprising at least one nuclearlocalization signal or nucleic acid encoding at least one RNA-guidedendonuclease as defined herein, (ii) at least one guide RNA or DNAencoding at least one guide RNA, and, optionally, (iii) at least onedonor polynucleotide comprising a donor sequence. The method furthercomprises culturing the cell or embryo such that each guide RNA directsa RNA-guided endonuclease to a targeted site in the chromosomal sequencewhere the RNA-guided endonuclease introduces a double-stranded break inthe targeted site, and the double-stranded break is repaired by a DNArepair process such that the chromosomal sequence is modified. In oneembodiment, the RNA-guided endonuclease can be derived from a Cas9protein. In another embodiment, the nucleic acid encoding the RNA-guidedendonuclease introduced into the cell or embryo can be mRNA. In afurther embodiment, wherein the nucleic acid encoding the RNA-guidedendonuclease introduced into the cell or embryo can be DNA. In a furtherembodiment, the DNA encoding the RNA-guided endonuclease can be part ofa vector that further comprises a sequence encoding the guide RNA. Incertain embodiments, the eukaryotic cell can be a human cell, anon-human mammalian cell, a stem cell, a non-mammalian vertebrate cell,an invertebrate cell, a plant cell, or a single cell eukaryoticorganism. In certain other embodiments, the embryo is a non-human onecell animal embryo.

A further aspect of the disclosure provides a fusion protein comprisinga CRISPR/Cas-like protein or fragment thereof and an effector domain. Ingeneral, the fusion protein comprises at least one nuclear localizationsignal. The effector domain of the fusion protein can be a cleavagedomain, an epigenetic modification domain, a transcriptional activationdomain, or a transcriptional repressor domain. In one embodiment, theCRISPR/Cas-like protein of the fusion protein can be derived from a Cas9protein. In one iteration, the Cas9 protein can be modified to lack atleast one functional nuclease domain. In an alternate iteration, theCas9 protein can be modified to lack all nuclease activity. In oneembodiment, the effector domain can be a cleavage domain, such as, forexample, a FokI endonuclease domain or a modified FokI endonucleasedomain. In another embodiment, one fusion protein can form a dimer withanother fusion protein. The dimer can be a homodimer or a heterodimer.In another embodiment, the fusion protein can form a heterodimer with azinc finger nuclease, wherein the cleavage domain of both the fusionprotein and the zinc finger nucleases is a FokI endonuclease domain or amodified FokI endonuclease domain. In still another embodiment, thefusion protein comprises a CRISPR/Cas-like protein derived from a Cas9protein modified to lack all nuclease activity, and the effector domainis a FokI endonuclease domain or a modified FokI endonuclease domain. Instill another embodiment, the fusion protein comprises a CRISPR/Cas-likeprotein derived from a Cas9 protein modified to lack all nucleaseactivity, and the effector domain can be an epigenetic modificationdomain, a transcriptional activation domain, or a transcriptionalrepressor domain. In additional embodiments, any of the fusion proteinsdisclosed herein can comprise at least one additional domain chosen froma nuclear localization signal, a cell-penetrating domain, and a markerdomain. Also provided are isolated nucleic acids encoding any of thefusion proteins provided herein.

Still another aspect of the disclosure encompasses a method formodifying a chromosomal sequence or regulating expression of achromosomal sequence in a cell or embryo. The method comprisesintroducing into the cell or embryo (a) at least one fusion protein ornucleic acid encoding at least one fusion protein, wherein the fusionprotein comprises a CRISPR/Cas-like protein or a fragment thereof and aneffector domain, and (b) at least one guide RNA or DNA encoding at leastone guide RNA, wherein the guide RNA guides the CRISPR/Cas-like proteinof the fusion protein to a targeted site in the chromosomal sequence andthe effector domain of the fusion protein modifies the chromosomalsequence or regulates expression of the chromosomal sequence. In oneembodiment, the CRISPR/Cas-like protein of the fusion protein can bederived from a Cas9 protein. In another embodiment, the CRISPR/Cas-likeprotein of the fusion protein can be modified to lack at least onefunctional nuclease domain. In still another embodiment, theCRISPR/Cas-like protein of the fusion protein can be modified to lackall nuclease activity. In one embodiment in which the fusion proteincomprises a Cas9 protein modified to lack all nuclease activity and aFokI cleavage domain or a modified FokI cleavage domain, the method cancomprise introducing into the cell or embryo one fusion protein ornucleic acid encoding one fusion protein and two guide RNAs or DNAencoding two guide RNAs, and wherein one double-stranded break isintroduced in the chromosomal sequence. In another embodiment in whichthe fusion protein comprises a Cas9 protein modified to lack allnuclease activity and a FokI cleavage domain or a modified FokI cleavagedomain, the method can comprise introducing into the cell or embryo twofusion proteins or nucleic acid encoding two fusion proteins and twoguide RNAs or DNA encoding two guide RNAs, and wherein twodouble-stranded breaks are introduced in the chromosomal sequence. Instill another one embodiment in which the fusion protein comprises aCas9 protein modified to lack all nuclease activity and a FokI cleavagedomain or a modified FokI cleavage domain, the method can compriseintroducing into the cell or embryo one fusion protein or nucleic acidencoding one fusion protein, one guide RNA or nucleic acid encoding oneguide RNA, and one zinc finger nuclease or nucleic acid encoding onezinc finger nuclease, wherein the zinc finger nuclease comprises a FokIcleavage domain or a modified a FokI cleavage domain, and wherein onedouble-stranded break is introduced into the chromosomal sequence. Incertain embodiments in which the fusion protein comprises a cleavagedomain, the method can further comprise introducing into the cell orembryo at least one donor polynucleotide. In embodiments in which thefusion protein comprises an effector domain chosen from an epigeneticmodification domain, a transcriptional activation domain, or atranscriptional repressor domain, the fusion protein can comprise a Cas9protein modified to lack all nuclease activity, and the method cancomprise introducing into the cell or embryo one fusion protein ornucleic acid encoding one fusion protein, and one guide RNA or nucleicacid encoding one guide RNA, and wherein the structure or expression ofthe targeted chromosomal sequence is modified. In certain embodiments,the eukaryotic cell can be a human cell, a non-human mammalian cell, astem cell, a non-mammalian vertebrate cell, an invertebrate cell, aplant cell, or a single cell eukaryotic organism. In certain otherembodiments, the embryo is a non-human one cell animal embryo.

Other aspects and iterations of the disclosure are detailed below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 diagrams genome modification using protein dimers. (A) depicts adouble stranded break created by a dimer composed of two fusionproteins, each of which comprises a Cas-like protein for DNA binding anda FokI cleavage domain. (B) depicts a double stranded break created by adimer composed of a fusion protein comprising a Cas-like protein and aFokI cleavage domain and a zinc finger nuclease comprising a zinc finger(ZF) DNA-binding domain and a FokI cleavage domain.

FIG. 2 illustrates regulation of gene expression using RNA-guided fusionproteins comprising gene regulatory domains. (A) depicts a fusionprotein comprising a Cas-like protein used for DNA binding and an “AIR”domain that activates or represses gene expression. (B) diagrams afusion protein comprising a Cas-like protein for DNA binding and aepigenetic modification domain (“Epi-mod”) that affects epigeneticstates by covalent modification of proximal DNA or proteins.

FIG. 3 diagrams genome modification using two RNA-guided endonuclease.(A) depicts a double stranded break created by two RNA-guidedendonuclease that have been converted into nickases. (B) depicts twodouble stranded breaks created by two RNA-guided endonuclease havingendonuclease activity.

FIG. 4 presents fluorescence-activated cell sorting (FACS) of human K562cells transfected with Cas9 nucleic acid, Cas9 guiding RNA, andAAVS1-GFP DNA donor. The Y axis represents the auto fluorescenceintensity at a red channel, and the X axis represents the greenfluorescence intensity. (A) K562 cells transfected with 10 μg of Cas9mRNA transcribed with an Anti-Reverse Cap Analog, 0.3 nmol ofpre-annealed crRNA-tracrRNA duplex, and 10 μg of AAVS1-GFP plasmid DNA;(B) K562 cells transfected 10 μg of Cas9 mRNA transcribed with anAnti-Reverse Cap Analog, 0.3 nmol of chimeric RNA, and 10 μg ofAAVS1-GFP plasmid DNA; (C) K562 cells transfected 10 μg of Cas9 mRNAthat was capped by post-transcription capping reaction, 0.3 nmol ofchimeric RNA, and 10 μg of AAVS1-GFP plasmid DNA; (D) K562 cellstransfected with 10 μg of Cas9 plasmid DNA, 5 μg of U6-chimeric RNAplasmid DNA, and 10 μg of AAVS1-GFP plasmid DNA; (E) K562 cellstransfected with 10 μg of AAVS1-GFP plasmid DNA; (F) K562 cellstransfected with transfection reagents only.

FIG. 5 presents a junction PCR analysis documenting the targetedintegration of GFP into the AAVS1 locus in human cells. Lane M: 1 kb DNAmolecular markers; Lane A: K562 cells transfected with 10 μg of Cas9mRNA transcribed with an Anti-Reverse Cap Analog, 0.3 nmol ofpre-annealed crRNA-tracrRNA duplex, and 10 μg of AAVS1-GFP plasmid DNA;Lane B: K562 cells transfected 10 μg of Cas9 mRNA transcribed with anAnti-Reverse Cap Analog, 0.3 nmol of chimeric RNA, and 10 μg ofAAVS1-GFP plasmid DNA; Lane C: K562 cells transfected 10 μg of Cas9 mRNAthat was capped by post-transcription capping reaction, 0.3 nmol ofchimeric RNA, and 10 μg of AAVS1-GFP plasmid DNA; Lane D: K562 cellstransfected with 10 μg of Cas9 plasmid DNA, 5 μg of U6-chimeric RNAplasmid DNA, and 10 μg of AAVS1-GFP plasmid DNA; Lane E: K562 cellstransfected with 10 μg of AAVS1-GFP plasmid DNA; Lane F: K562 cellstransfected with transfection reagents only.

DETAILED DESCRIPTION OF THE INVENTION

Provided herein are RNA-guided endonucleases, which comprise at leastone nuclear localization signal, at least one nuclease domain, and atleast one domain that interacts with a guide RNA to target theendonuclease to a specific nucleotide sequence for cleavage. Alsoprovided are nucleic acids encoding the RNA-guided endonucleases, aswell as methods of using the RNA-guided endonucleases to modifychromosomal sequences of eukaryotic cells or embryos. The RNA-guidedendonuclease interacts with specific guide RNAs, each of which directsthe endonuclease to a specific targeted site, at which site theRNA-guided endonuclease introduces a double-stranded break that can berepaired by a DNA repair process such that the chromosomal sequence ismodified. Since the specificity is provided by the guide RNA, theRNA-based endonuclease is universal and can be used with different guideRNAs to target different genomic sequences. The methods disclosed hereincan be used to target and modify specific chromosomal sequences and/orintroduce exogenous sequences at targeted locations in the genome ofcells or embryos. Furthermore, the targeting is specific with limitedoff target effects.

The present disclosure provides fusion proteins, wherein a fusionprotein comprises a CRISPR/Cas-like protein or fragment thereof and aneffector domain. Suitable effector domains include, without limit,cleavage domains, epigenetic modification domains, transcriptionalactivation domains, and transcriptional repressor domains. Each fusionprotein is guided to a specific chromosomal sequence by a specific guideRNA, wherein the effector domain mediates targeted genome modificationor gene regulation. In one aspect, the fusion proteins can function asdimers thereby increasing the length of the target site and increasingthe likelihood of its uniqueness in the genome (thus, reducing offtarget effects). For example, endogenous CRISPR systems modify genomiclocations based on DNA binding word lengths of approximately 13-20 bp(Cong et al., Science, 339:819-823). At this word size, only 5-7% of thetarget sites are unique within the genome (Iseli et al, PLos One 2(6):e579). In contrast, DNA binding word sizes for zinc finger nucleasestypically range from 30-36 bp, resulting in target sites that areapproximately 85-87% unique within the human genome. The smaller sizedDNA binding sites utilized by CRISPR-based systems limits andcomplicates design of targeted CRISP-based nucleases near desiredlocations, such as disease SNPs, small exons, start codons, and stopcodons, as well as other locations within complex genomes. The presentdisclosure not only provides means for expanding the CRISPR DNA bindingword length (i.e., so as to limit off-target activity), but furtherprovides CRISPR fusion proteins having modified functionality.According, the disclosed CRISPR fusion proteins have increased targetspecificity and unique functionality(ies). Also provided herein aremethods of using the fusion proteins to modify or regulate expression oftargeted chromosomal sequences.

(I) RNA-Guided Endonucleases

One aspect of the present disclosure provides RNA-guided endonucleasescomprising at least one nuclear localization signal, which permits entryof the endonuclease into the nuclei of eukaryotic cells and embryos suchas, for example, non-human one cell embryos. RNA-guided endonucleasesalso comprise at least one nuclease domain and at least one domain thatinteracts with a guide RNA. An RNA-guided endonuclease is directed to aspecific nucleic acid sequence (or target site) by a guide RNA. Theguide RNA interacts with the RNA-guided endonuclease as well as thetarget site such that, once directed to the target site, the RNA-guidedendonuclease is able to introduce a double-stranded break into thetarget site nucleic acid sequence. Since the guide RNA provides thespecificity for the targeted cleavage, the endonuclease of theRNA-guided endonuclease is universal and can be used with differentguide RNAs to cleave different target nucleic acid sequences. Providedherein are isolated RNA-guided endonucleases, isolated nucleic acids(i.e., RNA or DNA) encoding the RNA-guided endonucleases, vectorscomprising nucleic acids encoding the RNA-guided endonucleases, andprotein-RNA complexes comprising the RNA-guided endonuclease plus aguide RNA.

The RNA-guided endonuclease can be derived from a clustered regularlyinterspersed short palindromic repeats (CRISPR)/CRISPR-associated (Cas)system. The CRISPR/Cas system can be a type I, a type II, or a type IIIsystem. Non-limiting examples of suitable CRISPR/Cas proteins includeCas3, Cas4, Cas5, Cas5e (or CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8a1,Cas8a2, Cas8b, Cas8c, Cas9, Cas10, Cas10d, CasF, CasG, CasH, Csy1, Csy2,Csy3, Cse1 (or CasA), Cse2 (or CasB), Cse3 (or CasE), Cse4 (or CasC),Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4,Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3,Csz1, Csx15, Csf1, Csf2, Csf3, Csf4, and Cu1966.

In one embodiment, the RNA-guided endonuclease is derived from a type IICRISPR/Cas system. In specific embodiments, the RNA-guided endonucleaseis derived from a Cas9 protein. The Cas9 protein can be fromStreptococcus pyogenes, Streptococcus thermophilus, Streptococcus sp.,Nocardiopsis dassonvillei, Streptomyces pristinaespiralis, Streptomycesviridochromogenes, Streptomyces viridochromogenes, Streptosporangiumroseum, Streptosporangium roseum, Alicyclobacillus acidocaldarius,Bacillus pseudomycoides, Bacillus selenitireducens, Exiguobacteriumsibiricum, Lactobacillus delbrueckii, Lactobacillus salivarius,Microscilla marina, Burkholderiales bacterium, Polaromonasnaphthalenivorans, Polaromonas sp., Crocosphaera watsonii, Cyanothecesp., Microcystis aeruginosa, Synechococcus sp., Acetohalobiumarabaticum, Ammonifex degensii, Caldicelulosiruptor becscii, CandidatusDesulforudis, Clostridium botulinum, Clostridium difficile, Finegoldiamagna, Natranaerobius thermophilus, Pelotomaculum thermopropionicum,Acidithiobacillus caldus, Acidithiobacillus ferrooxidans, Allochromatiumvinosum, Marinobacter sp., Nitrosococcus halophilus, Nitrosococcuswatsoni, Pseudoalteromonas haloplanktis, Ktedonobacter racemifer,Methanohalobium evestigatum, Anabaena variabilis, Nodularia spumigena,Nostoc sp., Arthrospira maxima, Arthrospira platensis, Arthrospira sp.,Lyngbya sp., Microcoleus chthonoplastes, Oscillatoria sp., Petrotogamobilis, Thermosipho africanus, or Acaryochloris marina.

In general, CRISPR/Cas proteins comprise at least one RNA recognitionand/or RNA binding domain. RNA recognition and/or RNA binding domainsinteract with guide RNAs. CRISPR/Cas proteins can also comprise nucleasedomains (i.e., DNase or RNase domains), DNA binding domains, helicasedomains, RNAse domains, protein-protein interaction domains,dimerization domains, as well as other domains.

The CRISPR/Cas-like protein can be a wild type CRISPR/Cas protein, amodified CRISPR/Cas protein, or a fragment of a wild type or modifiedCRISPR/Cas protein. The CRISPR/Cas-like protein can be modified toincrease nucleic acid binding affinity and/or specificity, alter anenzymatic activity, and/or change another property of the protein. Forexample, nuclease (i.e., DNase, RNase) domains of the CRISPR/Cas-likeprotein can be modified, deleted, or inactivated. Alternatively, theCRISPR/Cas-like protein can be truncated to remove domains that are notessential for the function of the fusion protein. The CRISPR/Cas-likeprotein can also be truncated or modified to optimize the activity ofthe effector domain of the fusion protein.

In some embodiments, the CRISPR/Cas-like protein can be derived from awild type Cas9 protein or fragment thereof. In other embodiments, theCRISPR/Cas-like protein can be derived from modified Cas9 protein. Forexample, the amino acid sequence of the Cas9 protein can be modified toalter one or more properties (e.g., nuclease activity, affinity,stability, etc.) of the protein. Alternatively, domains of the Cas9protein not involved in RNA-guided cleavage can be eliminated from theprotein such that the modified Cas9 protein is smaller than the wildtype Cas9 protein.

In general, a Cas9 protein comprises at least two nuclease (i.e., DNase)domains. For example, a Cas9 protein can comprise a RuvC-like nucleasedomain and a HNH-like nuclease domain. The RuvC and HNH domains worktogether to cut single strands to make a double-stranded break in DNA.(Jinek et al., Science, 337: 816-821). In some embodiments, theCas9-derived protein can be modified to contain only one functionalnuclease domain (either a RuvC-like or a HNH-like nuclease domain). Forexample, the Cas9-derived protein can be modified such that one of thenuclease domains is deleted or mutated such that it is no longerfunctional (i.e., the nuclease activity is absent). In some embodimentsin which one of the nuclease domains is inactive, the Cas9-derivedprotein is able to introduce a nick into a double-stranded nucleic acid(such protein is termed a “nickase”), but not cleave the double-strandedDNA. For example, an aspartate to alanine (D10A) conversion in aRuvC-like domain converts the Cas9-derived protein into a nickase.Likewise, a histidine to alanine (H840A or H839A) conversion in a HNHdomain converts the Cas9-derived protein into a nickase. Each nucleasedomain can be modified using well-known methods, such as site-directedmutagenesis, PCR-mediated mutagenesis, and total gene synthesis, as wellas other methods known in the art.

The RNA-guided endonuclease disclosed herein comprises at least onenuclear localization signal. In general, an NLS comprises a stretch ofbasic amino acids. Nuclear localization signals are known in the art(see, e.g., Lange et al., J. Biol. Chem., 2007, 282:5101-5105). Forexample, in one embodiment, the NLS can be a monopartite sequence, suchas PKKKRKV (SEQ ID NO:1) or PKKKRRV (SEQ ID NO:2). In anotherembodiment, the NLS can be a bipartite sequence. In still anotherembodiment, the NLS can be KRPAATKKAGQAKKKK (SEQ ID NO:3). The NLS canbe located at the N-terminus, the C-terminal, or in an internal locationof the RNA-guided endonuclease.

In some embodiments, the RNA-guided endonuclease can further comprise atleast one cell-penetrating domain. In one embodiment, thecell-penetrating domain can be a cell-penetrating peptide sequencederived from the HIV-1 TAT protein. As an example, the TATcell-penetrating sequence can be GRKKRRQRRRPPQPKKKRKV (SEQ ID NO:4). Inanother embodiment, the cell-penetrating domain can be TLM(PLSSIFSRIGDPPKKKRKV; SEQ ID NO:5), a cell-penetrating peptide sequencederived from the human hepatitis B virus. In still another embodiment,the cell-penetrating domain can be MPG (GALFLGWLGAAGSTMGAPKKKRKV; SEQ IDNO:6 or GALFLGFLGAAGSTMGAWSQPKKKRKV; SEQ ID NO:7). In an additionalembodiment, the cell-penetrating domain can be Pep-1(KETWWETWWTEWSQPKKKRKV; SEQ ID NO:8), VP22, a cell penetrating peptidefrom Herpes simplex virus, or a polyarginine peptide sequence. Thecell-penetrating domain can be located at the N-terminus, theC-terminus, or in an internal location of the protein.

In still other embodiments, the RNA-guided endonuclease can alsocomprise at least one marker domain. Non-limiting examples of markerdomains include fluorescent proteins, purification tags, and epitopetags. In some embodiments, the marker domain can be a fluorescentprotein. Non limiting examples of suitable fluorescent proteins includegreen fluorescent proteins (e.g., GFP, GFP-2, tagGFP, turboGFP, EGFP,Emerald, Azami Green, Monomeric Azami Green, CopGFP, AceGFP, ZsGreen1),yellow fluorescent proteins (e.g. YFP, EYFP, Citrine, Venus, YPet,PhiYFP, ZsYellow1), blue fluorescent proteins (e.g. EBFP, EBFP2,Azurite, mKalama1, GFPuv, Sapphire, T-sapphire), cyan fluorescentproteins (e.g. ECFP, Cerulean, CyPet, AmCyan1, Midoriishi-Cyan), redfluorescent proteins (mKate, mKate2, mPlum, DsRed monomer, mCherry,mRFP1, DsRed-Express, DsRed2, DsRed-Monomer, HcRed-Tandem, HcRed1,AsRed2, eqFP611, mRasberry, mStrawberry, Jred), and orange fluorescentproteins (mOrange, mKO, Kusabira-Orange, Monomeric Kusabira-Orange,mTangerine, tdTomato) or any other suitable fluorescent protein. Inother embodiments, the marker domain can be a purification tag and/or anepitope tag. Exemplary tags include, but are not limited to,glutathione-S-transferase (GST), chitin binding protein (CBP), maltosebinding protein, thioredoxin (TRX), poly(NANP), tandem affinitypurification (TAP) tag, myc, AcV5, AU1, AU5, E, ECS, E2, FLAG, HA, nus,Softag 1, Softag 3, Strep, SBP, Glu-Glu, HSV, KT3, S, S1, T7, V5, VSV-G,6×His, biotin carboxyl carrier protein (BCCP), and calmodulin.

In certain embodiments, the RNA-guided endonuclease may be part of aprotein-RNA complex comprising a guide RNA. The guide RNA interacts withthe RNA-guided endonuclease to direct the endonuclease to a specifictarget site, wherein the 5′ end of the guide RNA base pairs with aspecific protospacer sequence.

(II) Fusion Proteins

Another aspect of the present disclosure provides a fusion proteincomprising a CRISPR/Cas-like protein or fragment thereof and an effectordomain. The CRISPR/Cas-like protein is directed to a target site by aguide RNA, at which site the effector domain can modify or effect thetargeted nucleic acid sequence. The effector domain can be a cleavagedomain, an epigenetic modification domain, a transcriptional activationdomain, or a transcriptional repressor domain. The fusion protein canfurther comprise at least one additional domain chosen from a nuclearlocalization signal, a cell-penetrating domain, or a marker domain.

(a) CRISPR/Cas-Like Protein

The fusion protein comprises a CRISPR/Cas-like protein or a fragmentthereof. CRISPR/Cas-like proteins are detailed above in section (I). TheCRISPR/Cas-like protein can be located at the N-terminus, theC-terminus, or in an internal location of the fusion protein

In some embodiments, the CRISPR/Cas-like protein of the fusion proteincan be derived from a Cas9 protein. The Cas9-derived protein can be wildtype, modified, or a fragment thereof. In some embodiments, theCas9-derived protein can be modified to contain only one functionalnuclease domain (either a RuvC-like or a HNH-like nuclease domain). Forexample, the Cas9-derived protein can be modified such that one of thenuclease domains is deleted or mutated such that it is no longerfunctional (i.e., the nuclease activity is absent). In some embodimentsin which one of the nuclease domains is inactive, the Cas9-derivedprotein is able to introduce a nick into a double-stranded nucleic acid(such protein is termed a “nickase”), but not cleave the double-strandedDNA. For example, an aspartate to alanine (D10A) conversion in aRuvC-like domain converts the Cas9-derived protein into a nickase.Likewise, a histidine to alanine (H840A or H839A) conversion in a HNHdomain converts the Cas9-derived protein into a nickase. In otherembodiments, both of the RuvC-like nuclease domain and the HNH-likenuclease domain can be modified or eliminated such that the Cas9-derivedprotein is unable to nick or cleave double stranded nucleic acid. Instill other embodiments, all nuclease domains of the Cas9-derivedprotein can be modified or eliminated such that the Cas9-derived proteinlacks all nuclease activity.

In any of the above-described embodiments, any or all of the nucleasedomains can be inactivated by one or more deletion mutations, insertionmutations, and/or substitution mutations using well-known methods, suchas site-directed mutagenesis, PCR-mediated mutagenesis, and total genesynthesis, as well as other methods known in the art. In an exemplaryembodiment, the CRISPR/Cas-like protein of the fusion protein is derivedfrom a Cas9 protein in which all the nuclease domains have beeninactivated or deleted.

(b) Effector Domain

The fusion protein also comprises an effector domain. The effectordomain can be a cleavage domain, an epigenetic modification domain, atranscriptional activation domain, or a transcriptional repressordomain. The effector domain can be located at the N-terminus, theC-terminus, or in an internal location of the fusion protein.

(i) Cleavage Domain

In some embodiments, the effector domain is a cleavage domain. As usedherein, a “cleavage domain” refers to a domain that cleaves DNA. Thecleavage domain can be obtained from any endonuclease or exonuclease.Non-limiting examples of endonucleases from which a cleavage domain canbe derived include, but are not limited to, restriction endonucleasesand homing endonucleases. See, for example, New England Biolabs Catalogor Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388. Additionalenzymes that cleave DNA are known (e.g., S1 Nuclease; mung beannuclease; pancreatic DNase I; micrococcal nuclease; yeast HOendonuclease). See also Linn et al. (eds.) Nucleases, Cold Spring HarborLaboratory Press, 1993. One or more of these enzymes (or functionalfragments thereof) can be used as a source of cleavage domains.

In some embodiments, the cleavage domain can be derived from a type II-Sendonuclease. Type II-S endonucleases cleave DNA at sites that aretypically several base pairs away the recognition site and, as such,have separable recognition and cleavage domains. These enzymes generallyare monomers that transiently associate to form dimers to cleave eachstrand of DNA at staggered locations. Non-limiting examples of suitabletype II-S endonucleases include BfiI, BpmI, BsaI, BsgI, BsmBI, BsmI,BspMI, FokI, MbolI, and SapI. In exemplary embodiments, the cleavagedomain of the fusion protein is a FokI cleavage domain or a derivativethereof.

In certain embodiments, the type II-S cleavage can be modified tofacilitate dimerization of two different cleavage domains (each of whichis attached to a CRISPR/Cas-like protein or fragment thereof). Forexample, the cleavage domain of FokI can be modified by mutating certainamino acid residues. By way of non-limiting example, amino acid residuesat positions 446, 447, 479, 483, 484, 486, 487, 490, 491, 496, 498, 499,500, 531, 534, 537, and 538 of FokI cleavage domains are targets formodification. For example, modified cleavage domains of FokI that formobligate heterodimers include a pair in which a first modified cleavagedomain includes mutations at amino acid positions 490 and 538 and asecond modified cleavage domain that includes mutations at amino acidpositions 486 and 499 (Miller et al., 2007, Nat. Biotechnol, 25:778-785;Szczpek et al., 2007, Nat. Biotechnol, 25:786-793). For example, the Glu(E) at position 490 can be changed to Lys (K) and the Ile (I) atposition 538 can be changed to K in one domain (E490K, I538K), and theGln (Q) at position 486 can be changed to E and the I at position 499can be changed to Leu (L) in another cleavage domain (Q486E, I499L). Inother embodiments, modified FokI cleavage domains can include threeamino acid changes (Doyon et al. 2011, Nat. Methods, 8:74-81). Forexample, one modified FokI domain (which is termed ELD) can compriseQ486E, I499L, N496D mutations and the other modified FokI domain (whichis termed KKR) can comprise E490K, I538K, H537R mutations.

In exemplary embodiments, the effector domain of the fusion protein is aFokI cleavage domain or a modified FokI cleavage domain.

In embodiments wherein the effector domain is a cleavage domain and theCRISPR/Cas-like protein is derived from a Cas9 protein, the Cas9-derivedcan be modified as discussed herein such that its endonuclease activityis eliminated. For example, the Cas9-derived can be modified by mutatingthe RuvC and HNH domains such that they no longer possess nucleaseactivity.

(ii) Epigenetic Modification Domain

In other embodiments, the effector domain of the fusion protein can bean epigenetic modification domain. In general, epigenetic modificationdomains alter histone structure and/or chromosomal structure withoutaltering the DNA sequence. Changes histone and/or chromatin structurecan lead to changes in gene expression. Examples of epigeneticmodification include, without limit, acetylation or methylation oflysine residues in histone proteins, and methylation of cytosineresidues in DNA. Non-limiting examples of suitable epigeneticmodification domains include histone acetyltansferase domains, histonedeacetylase domains, histone methyltransferase domains, histonedemethylase domains, DNA methyltransferase domains, and DNA demethylasedomains.

In embodiments in which the effector domain is a histoneacetyltansferase (HAT) domain, the HAT domain can be derived from EP300(i.e., E1A binding protein p300), CREBBP (i.e., CREB-binding protein),CDY1, CDY2, CDYL1, CLOCK, ELP3, ESA1, GCN5 (KAT2A), HAT1, KAT2B, KAT5,MYST1, MYST2, MYST3, MYST4, NCOA1, NCOA2, NCOA3, NCOAT, P/CAF, Tip60,TAFII250, or TF3C4. In one such embodiment, the HAT domain is p300

In embodiments wherein the effector domain is an epigenetic modificationdomain and the CRISPR/Cas-like protein is derived from a Cas9 protein,the Cas9-derived can be modified as discussed herein such that itsendonuclease activity is eliminated. For example, the Cas9-derived canbe modified by mutating the RuvC and HNH domains such that they nolonger possess nuclease activity.

(iii) Transcriptional Activation Domain

In other embodiments, the effector domain of the fusion protein can be atranscriptional activation domain. In general, a transcriptionalactivation domain interacts with transcriptional control elements and/ortranscriptional regulatory proteins (i.e., transcription factors, RNApolymerases, etc.) to increase and/or activate transcription of a gene.In some embodiments, the transcriptional activation domain can be,without limit, a herpes simplex virus VP16 activation domain, VP64(which is a tetrameric derivative of VP16), a NFκB p65 activationdomain, p53 activation domains 1 and 2, a CREB (cAMP response elementbinding protein) activation domain, an E2A activation domain, and anNFAT (nuclear factor of activated T-cells) activation domain. In otherembodiments, the transcriptional activation domain can be Gal4, Gcn4,MLL, Rtg3, Gln3, Oaf1, Pip2, Pdr1, Pdr3, Pho4, and Leu3. Thetranscriptional activation domain may be wild type, or it may be amodified version of the original transcriptional activation domain. Insome embodiments, the effector domain of the fusion protein is a VP16 orVP64 transcriptional activation domain.

In embodiments wherein the effector domain is a transcriptionalactivation domain and the CRISPR/Cas-like protein is derived from a Cas9protein, the Cas9-derived protein can be modified as discussed hereinsuch that its endonuclease activity is eliminated. For example, theCas9-derived can be modified by mutating the RuvC and HNH domains suchthat they no longer possess nuclease activity.

(iv) Transcriptional Repressor Domain

In still other embodiments, the effector domain of the fusion proteincan be a transcriptional repressor domain. In general, a transcriptionalrepressor domain interacts with transcriptional control elements and/ortranscriptional regulatory proteins (i.e., transcription factors, RNApolymerases, etc.) to decrease and/or terminate transcription of a gene.Non-limiting examples of suitable transcriptional repressor domainsinclude inducible cAMP early repressor (ICER) domains,Kruppel-associated box A (KRAB-A) repressor domains, YY1 glycine richrepressor domains, Sp1-like repressors, E(spl) repressors, IκBrepressor, and MeCP2.

In embodiments wherein the effector domain is a transcriptionalrepressor domain and the CRISPR/Cas-like protein is derived from a Cas9protein, the Cas9-derived protein can be modified as discussed hereinsuch that its endonuclease activity is eliminated. For example, the cas9can be modified by mutating the RuvC and HNH domains such that they nolonger possess nuclease activity.

(c) Additional Domains

In some embodiments, the fusion protein further comprises at least oneadditional domain. Non-limiting examples of suitable additional domainsinclude nuclear localization signals, cell-penetrating or translocationdomains, and marker domains. Non-limiting examples of suitable nuclearlocalization signals, cell-penetrating domains, and marker domains arepresented above in section (I).

(d) Fusion Protein Dimers

In embodiments in which the effector domain of the fusion protein is acleavage domain, a dimer comprising at least one fusion protein canform. The dimer can be a homodimer or a heterodimer. In someembodiments, the heterodimer comprises two different fusion proteins. Inother embodiments, the heterodimer comprises one fusion protein and anadditional protein.

In some embodiments, the dimer is a homodimer in which the two fusionprotein monomers are identical with respect to the primary amino acidsequence. In one embodiment where the dimer is a homodimer, theCas9-derived proteins are modified such that their endonuclease activityis eliminated, i.e., such that they have no functional nuclease domains.In certain embodiments wherein the Cas9-derived proteins are modifiedsuch that their endonuclease activity is eliminated, each fusion proteinmonomer comprises an identical Cas9 like protein and an identicalcleavage domain. The cleavage domain can be any cleavage domain, such asany of the exemplary cleavage domains provided herein. In one specificembodiment, the cleavage domain is a FokI cleavage domain or a modifiedFokI cleavage domain. In such embodiments, specific guide RNAs woulddirect the fusion protein monomers to different but closely adjacentsites such that, upon dimer formation, the nuclease domains of the twomonomers would create a double stranded break in the target DNA.

In other embodiments, the dimer is a heterodimer of two different fusionproteins. For example, the CRISPR/Cas-like protein of each fusionprotein can be derived from a different CRISPR/Cas protein or from anorthologous CRISPR/Cas protein from a different bacterial species. Forexample, each fusion protein can comprise a Cas9-like protein, whichCas9-like protein is derived from a different bacterial species. Inthese embodiments, each fusion protein would recognize a differenttarget site (i.e., specified by the protospacer and/or PAM sequence).For example, the guide RNAs could position the heterodimer to differentbut closely adjacent sites such that their nuclease domains results inan effective double stranded break in the target DNA. The heterodimercan also have modified Cas9 proteins with nicking activity such that thenicking locations are different.

Alternatively, two fusion proteins of a heterodimer can have differenteffector domains. In embodiments in which the effector domain is acleavage domain, each fusion protein can contain a different modifiedcleavage domain. For example, each fusion protein can contain adifferent modified FokI cleavage domain, as detailed above in section(II)(b)(i). In these embodiments, the Cas-9 proteins can be modifiedsuch that their endonuclease activities are eliminated.

As will be appreciated by those skilled in the art, the two fusionproteins forming a heterodimer can differ in both the CRISPR/Cas-likeprotein domain and the effector domain.

In any of the above-described embodiments, the homodimer or heterodimercan comprise at least one additional domain chosen from nuclearlocalization signals (NLSs), cell-penetrating, translocation domains andmarker domains, as detailed above.

In any of the above-described embodiments, one or both of theCas9-derived proteins can be modified such that its endonucleaseactivity is eliminated or modified.

In still alternate embodiments, the heterodimer comprises one fusionprotein and an additional protein. For example, the additional proteincan be a nuclease. In one embodiment, the nuclease is a zinc fingernuclease. A zinc finger nuclease comprises a zinc finger DNA bindingdomain and a cleavage domain. A zinc finger recognizes and binds three(3) nucleotides. A zinc finger DNA binding domain can comprise fromabout three zinc fingers to about seven zinc fingers. The zinc fingerDNA binding domain can be derived from a naturally occurring protein orit can be engineered. See, for example, Beerli et al. (2002) Nat.Biotechnol. 20:135-141; Pabo et al. (2001) Ann. Rev. Biochem.70:313-340; Isalan et al. (2001) Nat. Biotechnol. 19:656-660; Segal etal. (2001) Curr. Opin. Biotechnol. 12:632-637; Choo et al. (2000) Curr.Opin. Struct. Biol. 10:411-416; Zhang et al. (2000) J. Biol. Chem.275(43):33850-33860; Doyon et al. (2008) Nat. Biotechnol. 26:702-708;and Santiago et al. (2008) Proc. Natl. Acad. Sci. USA 105:5809-5814. Thecleavage domain of the zinc finger nuclease can be any cleavage domaindetailed above in section (II)(b)(i). In exemplary embodiments, thecleavage domain of the zinc finger nuclease is a FokI cleavage domain ora modified FokI cleavage domain. Such a zinc finger nuclease willdimerize with a fusion protein comprising a FokI cleavage domain or amodified FokI cleavage domain.

In some embodiments, the zinc finger nuclease can comprise at least oneadditional domain chosen from nuclear localization signals,cell-penetrating or translocation domains, which are detailed above.

In certain embodiments, any of the fusion protein detailed above or adimer comprising at least one fusion protein may be part of aprotein-RNA complex comprising at least one guide RNA. A guide RNAinteracts with the CRISPR-Cas0 like protein of the fusion protein todirect the fusion protein to a specific target site, wherein the 5′ endof the guide RNA base pairs with a specific protospacer sequence.

(III) Nucleic Acids Encoding RNA-Guided Endonucleases or Fusion Proteins

Another aspect of the present disclosure provides nucleic acids encodingany of the RNA-guided endonucleases or fusion proteins described abovein sections (I) and (II), respectively. The nucleic acid can be RNA orDNA. In one embodiment, the nucleic acid encoding the RNA-guidedendonuclease or fusion protein is mRNA. The mRNA can be 5′ capped and/or3′ polyadenylated. In another embodiment, the nucleic acid encoding theRNA-guided endonuclease or fusion protein is DNA. The DNA can be presentin a vector (see below).

The nucleic acid encoding the RNA-guided endonuclease or fusion proteincan be codon optimized for efficient translation into protein in theeukaryotic cell or animal of interest. For example, codons can beoptimized for expression in humans, mice, rats, hamsters, cows, pigs,cats, dogs, fish, amphibians, plants, yeast, insects, and so forth (seeCodon Usage Database at www.kazusa.or.jp/codon/). Programs for codonoptimization are available as freeware (e.g., OPTIMIZER atgenomes.urv.es/OPTIMIZER; OptimumGene™ from GenScript atwww.genscript.com/codon_opt.html). Commercial codon optimizationprograms are also available.

In some embodiments, DNA encoding the RNA-guided endonuclease or fusionprotein can be operably linked to at least one promoter controlsequence. In some iterations, the DNA coding sequence can be operablylinked to a promoter control sequence for expression in the eukaryoticcell or animal of interest. The promoter control sequence can beconstitutive, regulated, or tissue-specific. Suitable constitutivepromoter control sequences include, but are not limited to,cytomegalovirus immediate early promoter (CMV), simian virus (SV40)promoter, adenovirus major late promoter, Rous sarcoma virus (RSV)promoter, mouse mammary tumor virus (MMTV) promoter, phosphoglyceratekinase (PGK) promoter, elongation factor (ED1)-alpha promoter, ubiquitinpromoters, actin promoters, tubulin promoters, immunoglobulin promoters,fragments thereof, or combinations of any of the foregoing. Examples ofsuitable regulated promoter control sequences include without limitthose regulated by heat shock, metals, steroids, antibiotics, oralcohol. Non-limiting examples of tissue-specific promoters include B29promoter, CD14 promoter, CD43 promoter, CD45 promoter, CD68 promoter,desmin promoter, elastase-1 promoter, endoglin promoter, fibronectinpromoter, Flt-1 promoter, GFAP promoter, GPIIb promoter, ICAM-2promoter, INF-β promoter, Mb promoter, NphsI promoter, 00-2 promoter,SP-B promoter, SYN1 promoter, and WASP promoter. The promoter sequencecan be wild type or it can be modified for more efficient or efficaciousexpression. In one exemplary embodiment, the encoding DNA can beoperably linked to a CMV promoter for constitutive expression inmammalian cells.

In certain embodiments, the sequence encoding the RNA-guidedendonuclease or fusion protein can be operably linked to a promotersequence that is recognized by a phage RNA polymerase for in vitro mRNAsynthesis. In such embodiments, the in vitro-transcribed RNA can bepurified for use in the methods detailed below in sections (IV) and (V).For example, the promoter sequence can be a T7, T3, or SP6 promotersequence or a variation of a T7, T3, or SP6 promoter sequence. In anexemplary embodiment, the DNA encoding the fusion protein is operablylinked to a T7 promoter for in vitro mRNA synthesis using T7 RNApolymerase.

In alternate embodiments, the sequence encoding the RNA-guidedendonuclease or fusion protein can be operably linked to a promotersequence for in vitro expression of the RNA-guided endonuclease orfusion protein in bacterial or eukaryotic cells. In such embodiments,the expressed protein can be purified for use in the methods detailedbelow in sections (IV) and (V). Suitable bacterial promoters include,without limit, T7 promoters, lac operon promoters, trp promoters,variations thereof, and combinations thereof. An exemplary bacterialpromoter is tac which is a hybrid of trp and lac promoters. Non-limitingexamples of suitable eukaryotic promoters are listed above.

In additional aspects, the DNA encoding the RNA-guided endonuclease orfusion protein also can be linked to a polyadenylation signal (e.g.,SV40 polyA signal, bovine growth hormone (BGH) polyA signal, etc.)and/or at least one transcriptional termination sequence. Additionally,the sequence encoding the RNA-guided endonuclease or fusion protein alsocan be linked to sequence encoding at least one nuclear localizationsignal, at least one cell-penetrating domain, and/or at least one markerdomain, which are detailed above in section (I).

In various embodiments, the DNA encoding the RNA-guided endonuclease orfusion protein can be present in a vector. Suitable vectors includeplasmid vectors, phagemids, cosmids, artificial/mini-chromosomes,transposons, and viral vectors (e.g., lentiviral vectors,adeno-associated viral vectors, etc.). In one embodiment, the DNAencoding the RNA-guided endonuclease or fusion protein is present in aplasmid vector. Non-limiting examples of suitable plasmid vectorsinclude pUC, pBR322, pET, pBluescript, and variants thereof. The vectorcan comprise additional expression control sequences (e.g., enhancersequences, Kozak sequences, polyadenylation sequences, transcriptionaltermination sequences, etc.), selectable marker sequences (e.g.,antibiotic resistance genes), origins of replication, and the like.Additional information can be found in “Current Protocols in MolecularBiology” Ausubel et al., John Wiley & Sons, New York, 2003 or “MolecularCloning: A Laboratory Manual” Sambrook & Russell, Cold Spring HarborPress, Cold Spring Harbor, N.Y., 3^(rd) edition, 2001.

In some embodiments, the expression vector comprising the sequenceencoding the RNA-guided endonuclease or fusion protein can furthercomprise sequence encoding a guide RNA. The sequence encoding the guideRNA generally is operably linked to at least one transcriptional controlsequence for expression of the guide RNA in the cell or embryo ofinterest. For example, DNA encoding the guide RNA can be operably linkedto a promoter sequence that is recognized by RNA polymerase III (PolIII). Examples of suitable Pol III promoters include, but are notlimited to, mammalian U6, U3, H1, and 7SL RNA promoters.

(IV) Method for Modifying a Chromosomal Sequence Using an RNA-GuidedEndonuclease

Another aspect of the present disclosure encompasses a method formodifying a chromosomal sequence in a eukaryotic cell or embryo. Themethod comprises introducing into a eukaryotic cell or embryo (i) atleast one RNA-guided endonuclease comprising at least one nuclearlocalization signal or nucleic acid encoding at least one RNA-guidedendonuclease comprising at least one nuclear localization signal, (ii)at least one guide RNA or DNA encoding at least one guide RNA, and,optionally, (iii) at least one donor polynucleotide comprising a donorsequence. The method further comprises culturing the cell or embryo suchthat each guide RNA directs an RNA-guided endonuclease to a targetedsite in the chromosomal sequence where the RNA-guided endonucleaseintroduces a double-stranded break in the targeted site, and thedouble-stranded break is repaired by a DNA repair process such that thechromosomal sequence is modified.

In some embodiments, the method can comprise introducing one RNA-guidedendonuclease (or encoding nucleic acid) and one guide RNA (or encodingDNA) into a cell or embryo, wherein the RNA-guided endonucleaseintroduces one double-stranded break in the targeted chromosomalsequence. In embodiments in which the optional donor polynucleotide isnot present, the double-stranded break in the chromosomal sequence canbe repaired by a non-homologous end-joining (NHEJ) repair process.Because NHEJ is error-prone, deletions of at least one nucleotide,insertions of at least one nucleotide, substitutions of at least onenucleotide, or combinations thereof can occur during the repair of thebreak. Accordingly, the targeted chromosomal sequence can be modified orinactivated. For example, a single nucleotide change (SNP) can give riseto an altered protein product, or a shift in the reading frame of acoding sequence can inactivate or “knock out” the sequence such that noprotein product is made. In embodiments in which the optional donorpolynucleotide is present, the donor sequence in the donorpolynucleotide can be exchanged with or integrated into the chromosomalsequence at the targeted site during repair of the double-strandedbreak. For example, in embodiments in which the donor sequence isflanked by upstream and downstream sequences having substantial sequenceidentity with upstream and downstream sequences, respectively, of thetargeted site in the chromosomal sequence, the donor sequence can beexchanged with or integrated into the chromosomal sequence at thetargeted site during repair mediated by homology-directed repairprocess. Alternatively, in embodiments in which the donor sequence isflanked by compatible overhangs (or the compatible overhangs aregenerated in situ by the RNA-guided endonuclease) the donor sequence canbe ligated directly with the cleaved chromosomal sequence by anon-homologous repair process during repair of the double-strandedbreak. Exchange or integration of the donor sequence into thechromosomal sequence modifies the targeted chromosomal sequence orintroduces an exogenous sequence into the chromosomal sequence of thecell or embryo.

In other embodiments, the method can comprise introducing two RNA-guidedendonucleases (or encoding nucleic acid) and two guide RNAs (or encodingDNA) into a cell or embryo, wherein the RNA-guided endonucleasesintroduce two double-stranded breaks in the chromosomal sequence. SeeFIG. 3B. The two breaks can be within several base pairs, within tens ofbase pairs, or can be separated by many thousands of base pairs. Inembodiments in which the optional donor polynucleotide is not present,the resultant double-stranded breaks can be repaired by a non-homologousrepair process such that the sequence between the two cleavage sites islost and/or deletions of at least one nucleotide, insertions of at leastone nucleotide, substitutions of at least one nucleotide, orcombinations thereof can occur during the repair of the break(s). Inembodiments in which the optional donor polynucleotide is present, thedonor sequence in the donor polynucleotide can be exchanged with orintegrated into the chromosomal sequence during repair of thedouble-stranded breaks by either a homology-based repair process (e.g.,in embodiments in which the donor sequence is flanked by upstream anddownstream sequences having substantial sequence identity with upstreamand downstream sequences, respectively, of the targeted sites in thechromosomal sequence) or a non-homologous repair process (e.g., inembodiments in which the donor sequence is flanked by compatibleoverhangs).

In still other embodiments, the method can comprise introducing oneRNA-guided endonuclease modified to cleave one strand of adouble-stranded sequence (or encoding nucleic acid) and two guide RNAs(or encoding DNA) into a cell or embryo, wherein each guide RNA directsthe RNA-guided endonuclease to a specific target site, at which site themodified endonuclease cleaves one strand (i.e., nicks) of thedouble-stranded chromosomal sequence, and wherein the two nicks are inopposite stands and in close enough proximity to constitute adouble-stranded break. See FIG. 3A. In embodiments in which the optionaldonor polynucleotide is not present, the resultant double-stranded breakcan be repaired by a non-homologous repair process such that deletionsof at least one nucleotide, insertions of at least one nucleotide,substitutions of at least one nucleotide, or combinations thereof canoccur during the repair of the break. In embodiments in which theoptional donor polynucleotide is present, the donor sequence in thedonor polynucleotide can be exchanged with or integrated into thechromosomal sequence during repair of the double-stranded break byeither a homology-based repair process (e.g., in embodiments in whichthe donor sequence is flanked by upstream and downstream sequenceshaving substantial sequence identity with upstream and downstreamsequences, respectively, of the targeted sites in the chromosomalsequence) or a non-homologous repair process (e.g., in embodiments inwhich the donor sequence is flanked by compatible overhangs).

(a) RNA-Guided Endonuclease

The method comprises introducing into a cell or embryo at least oneRNA-guided endonuclease comprising at least one nuclear localizationsignal or nucleic acid encoding at least one RNA-guided endonucleasecomprising at least one nuclear localization signal. Such RNA-guidedendonucleases and nucleic acids encoding RNA-guided endonucleases aredescribed above in sections (I) and (III), respectively.

In some embodiments, the RNA-guided endonuclease can be introduced intothe cell or embryo as an isolated protein. In such embodiments, theRNA-guided endonuclease can further comprise at least onecell-penetrating domain, which facilitates cellular uptake of theprotein. In other embodiments, the RNA-guided endonuclease can beintroduced into the cell or embryo as an mRNA molecule. In still otherembodiments, the RNA-guided endonuclease can be introduced into the cellor embryo as a DNA molecule. In general, DNA sequence encoding thefusion protein is operably linked to a promoter sequence that willfunction in the cell or embryo of interest. The DNA sequence can belinear, or the DNA sequence can be part of a vector. In still otherembodiments, the fusion protein can be introduced into the cell orembryo as an RNA-protein complex comprising the fusion protein and theguide RNA.

In alternate embodiments, DNA encoding the RNA-guided endonuclease canfurther comprise sequence encoding a guide RNA. In general, each of thesequences encoding the RNA-guided endonuclease and the guide RNA isoperably linked to appropriate promoter control sequence that allowsexpression of the RNA-guided endonuclease and the guide RNA,respectively, in the cell or embryo. The DNA sequence encoding theRNA-guided endonuclease and the guide RNA can further compriseadditional expression control, regulatory, and/or processingsequence(s). The DNA sequence encoding the RNA-guided endonuclease andthe guide RNA can be linear or can be part of a vector

(b) Guide RNA

The method also comprises introducing into a cell or embryo at least oneguide RNA or DNA encoding at least one guide RNA. A guide RNA interactswith the RNA-guided endonuclease to direct the endonuclease to aspecific target site, at which site the 5′ end of the guide RNA basepairs with a specific protospacer sequence in the chromosomal sequence.

Each guide RNA comprises three regions: a first region at the 5′ endthat is complementary to the target site in the chromosomal sequence, asecond internal region that forms a stem loop structure, and a third 3′region that remains essentially single-stranded. The first region ofeach guide RNA is different such that each guide RNA guides a fusionprotein to a specific target site. The second and third regions of eachguide RNA can be the same in all guide RNAs.

The first region of the guide RNA is complementary to sequence (i.e.,protospacer sequence) at the target site in the chromosomal sequencesuch that the first region of the guide RNA can base pair with thetarget site. In various embodiments, the first region of the guide RNAcan comprise from about 10 nucleotides to more than about 25nucleotides. For example, the region of base pairing between the firstregion of the guide RNA and the target site in the chromosomal sequencecan be about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25,or more than 25 nucleotides in length. In an exemplary embodiment, thefirst region of the guide RNA is about 19, 20, or 21 nucleotides inlength.

The guide RNA also comprises a second region that forms a secondarystructure. In some embodiments, the secondary structure comprises a stem(or hairpin) and a loop. The length of the loop and the stem can vary.For example, the loop can range from about 3 to about 10 nucleotides inlength, and the stem can range from about 6 to about 20 base pairs inlength. The stem can comprise one or more bulges of 1 to about 10nucleotides. Thus, the overall length of the second region can rangefrom about 16 to about 60 nucleotides in length. In an exemplaryembodiment, the loop is about 4 nucleotides in length and the stemcomprises about 12 base pairs.

The guide RNA also comprises a third region at the 3′ end that remainsessentially single-stranded. Thus, the third region has nocomplementarity to any chromosomal sequence in the cell of interest andhas no complementarity to the rest of the guide RNA. The length of thethird region can vary. In general, the third region is more than about 4nucleotides in length. For example, the length of the third region canrange from about 5 to about 60 nucleotides in length.

The combined length of the second and third regions (also called theuniversal or scaffold region) of the guide RNA can range from about 30to about 120 nucleotides in length. In one aspect, the combined lengthof the second and third regions of the guide RNA range from about 70 toabout 100 nucleotides in length.

In some embodiments, the guide RNA comprises a single moleculecomprising all three regions. In other embodiments, the guide RNA cancomprise two separate molecules. The first RNA molecule can comprise thefirst region of the guide RNA and one half of the “stem” of the secondregion of the guide RNA. The second RNA molecule can comprise the otherhalf of the “stem” of the second region of the guide RNA and the thirdregion of the guide RNA. Thus, in this embodiment, the first and secondRNA molecules each contain a sequence of nucleotides that arecomplementary to one another. For example, in one embodiment, the firstand second RNA molecules each comprise a sequence (of about 6 to about20 nucleotides) that base pairs to the other sequence to form afunctional guide RNA.

In some embodiments, the guide RNA can be introduced into the cell orembryo as a RNA molecule. The RNA molecule can be transcribed in vitro.Alternatively, the RNA molecule can be chemically synthesized.

In other embodiments, the guide RNA can be introduced into the cell orembryo as a DNA molecule. In such cases, the DNA encoding the guide RNAcan be operably linked to promoter control sequence for expression ofthe guide RNA in the cell or embryo of interest. For example, the RNAcoding sequence can be operably linked to a promoter sequence that isrecognized by RNA polymerase III (Pol III). Examples of suitable Pol IIIpromoters include, but are not limited to, mammalian U6 or H1 promoters.In exemplary embodiments, the RNA coding sequence is linked to a mouseor human U6 promoter. In other exemplary embodiments, the RNA codingsequence is linked to a mouse or human H1 promoter.

The DNA molecule encoding the guide RNA can be linear or circular. Insome embodiments, the DNA sequence encoding the guide RNA can be part ofa vector. Suitable vectors include plasmid vectors, phagemids, cosmids,artificial/mini-chromosomes, transposons, and viral vectors. In anexemplary embodiment, the DNA encoding the RNA-guided endonuclease ispresent in a plasmid vector. Non-limiting examples of suitable plasmidvectors include pUC, pBR322, pET, pBluescript, and variants thereof. Thevector can comprise additional expression control sequences (e.g.,enhancer sequences, Kozak sequences, polyadenylation sequences,transcriptional termination sequences, etc.), selectable markersequences (e.g., antibiotic resistance genes), origins of replication,and the like.

In embodiments in which both the RNA-guided endonuclease and the guideRNA are introduced into the cell as DNA molecules, each can be part of aseparate molecule (e.g., one vector containing fusion protein codingsequence and a second vector containing guide RNA coding sequence) orboth can be part of the same molecule (e.g., one vector containingcoding (and regulatory) sequence for both the fusion protein and theguide RNA).

(c) Target Site

An RNA-guided endonuclease in conjunction with a guide RNA is directedto a target site in the chromosomal sequence, wherein the RNA-guidedendonuclease introduces a double-stranded break in the chromosomalsequence. The target site has no sequence limitation except that thesequence is immediately followed (downstream) by a consensus sequence.This consensus sequence is also known as a protospacer adjacent motif(PAM). Examples of PAM include, but are not limited to, NGG, NGGNG, andNNAGAAW (wherein N is defined as any nucleotide and W is defined aseither A or T). As detailed above in section (IV)(b), the first region(at the 5′ end) of the guide RNA is complementary to the protospacer ofthe target sequence. Typically, the first region of the guide RNA isabout 19 to 21 nucleotides in length. Thus, in certain aspects, thesequence of the target site in the chromosomal sequence is5′-N₁₉₋₂₁-NGG-3′. The PAM is in italics.

The target site can be in the coding region of a gene, in an intron of agene, in a control region of a gene, in a non-coding region betweengenes, etc. The gene can be a protein coding gene or an RNA coding gene.The gene can be any gene of interest.

(d) Optional Donor Polynucleotide

In some embodiments, the method further comprises introducing at leastone donor polynucleotide into the embryo. A donor polynucleotidecomprises at least one donor sequence. In some aspects, a donor sequenceof the donor polynucleotide corresponds to an endogenous or nativechromosomal sequence. For example, the donor sequence can be essentiallyidentical to a portion of the chromosomal sequence at or near thetargeted site, but which comprises at least one nucleotide change. Thus,the donor sequence can comprise a modified version of the wild typesequence at the targeted site such that, upon integration or exchangewith the native sequence, the sequence at the targeted chromosomallocation comprises at least one nucleotide change. For example, thechange can be an insertion of one or more nucleotides, a deletion of oneor more nucleotides, a substitution of one or more nucleotides, orcombinations thereof. As a consequence of the integration of themodified sequence, the cell or embryo/animal can produce a modified geneproduct from the targeted chromosomal sequence.

In other aspects, the donor sequence of the donor polynucleotidecorresponds to an exogenous sequence. As used herein, an “exogenous”sequence refers to a sequence that is not native to the cell or embryo,or a sequence whose native location in the genome of the cell or embryois in a different location. For example, the exogenous sequence cancomprise protein coding sequence, which can be operably linked to anexogenous promoter control sequence such that, upon integration into thegenome, the cell or embryo/animal is able to express the protein codedby the integrated sequence. Alternatively, the exogenous sequence can beintegrated into the chromosomal sequence such that its expression isregulated by an endogenous promoter control sequence. In otheriterations, the exogenous sequence can be a transcriptional controlsequence, another expression control sequence, an RNA coding sequence,and so forth. Integration of an exogenous sequence into a chromosomalsequence is termed a “knock in.”

As can be appreciated by those skilled in the art, the length of thedonor sequence can and will vary. For example, the donor sequence canvary in length from several nucleotides to hundreds of nucleotides tohundreds of thousands of nucleotides.

Donor Polynucleotide Comprising Upstream and Downstream Sequences.

In some embodiments, the donor sequence in the donor polynucleotide isflanked by an upstream sequence and a downstream sequence, which havesubstantial sequence identity to sequences located upstream anddownstream, respectively, of the targeted site in the chromosomalsequence. Because of these sequence similarities, the upstream anddownstream sequences of the donor polynucleotide permit homologousrecombination between the donor polynucleotide and the targetedchromosomal sequence such that the donor sequence can be integrated into(or exchanged with) the chromosomal sequence.

The upstream sequence, as used herein, refers to a nucleic acid sequencethat shares substantial sequence identity with a chromosomal sequenceupstream of the targeted site. Similarly, the downstream sequence refersto a nucleic acid sequence that shares substantial sequence identitywith a chromosomal sequence downstream of the targeted site. As usedherein, the phrase “substantial sequence identity” refers to sequenceshaving at least about 75% sequence identity. Thus, the upstream anddownstream sequences in the donor polynucleotide can have about 75%,76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identitywith sequence upstream or downstream to the targeted site. In anexemplary embodiment, the upstream and downstream sequences in the donorpolynucleotide can have about 95% or 100% sequence identity withchromosomal sequences upstream or downstream to the targeted site. Inone embodiment, the upstream sequence shares substantial sequenceidentity with a chromosomal sequence located immediately upstream of thetargeted site (i.e., adjacent to the targeted site). In otherembodiments, the upstream sequence shares substantial sequence identitywith a chromosomal sequence that is located within about one hundred(100) nucleotides upstream from the targeted site. Thus, for example,the upstream sequence can share substantial sequence identity with achromosomal sequence that is located about 1 to about 20, about 21 toabout 40, about 41 to about 60, about 61 to about 80, or about 81 toabout 100 nucleotides upstream from the targeted site. In oneembodiment, the downstream sequence shares substantial sequence identitywith a chromosomal sequence located immediately downstream of thetargeted site (i.e., adjacent to the targeted site). In otherembodiments, the downstream sequence shares substantial sequenceidentity with a chromosomal sequence that is located within about onehundred (100) nucleotides downstream from the targeted site. Thus, forexample, the downstream sequence can share substantial sequence identitywith a chromosomal sequence that is located about 1 to about 20, about21 to about 40, about 41 to about 60, about 61 to about 80, or about 81to about 100 nucleotides downstream from the targeted site.

Each upstream or downstream sequence can range in length from about 20nucleotides to about 5000 nucleotides. In some embodiments, upstream anddownstream sequences can comprise about 50, 100, 200, 300, 400, 500,600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700,1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2800, 3000, 3200,3400, 3600, 3800, 4000, 4200, 4400, 4600, 4800, or 5000 nucleotides. Inexemplary embodiments, upstream and downstream sequences can range inlength from about 50 to about 1500 nucleotides.

Donor polynucleotides comprising the upstream and downstream sequenceswith sequence similarity to the targeted chromosomal sequence can belinear or circular. In embodiments in which the donor polynucleotide iscircular, it can be part of a vector. For example, the vector can be aplasmid vector.

Donor Polynucleotide Comprising Targeted Cleavage Site(s).

In other embodiments, the donor polynucleotide can additionally compriseat least one targeted cleavage site that is recognized by the RNA-guidedendonuclease. The targeted cleavage site added to the donorpolynucleotide can be placed upstream or downstream or both upstream anddownstream of the donor sequence. For example, the donor sequence can beflanked by targeted cleavage sites such that, upon cleavage by theRNA-guided endonuclease, the donor sequence is flanked by overhangs thatare compatible with those in the chromosomal sequence generated uponcleavage by the RNA-guided endonuclease. Accordingly, the donor sequencecan be ligated with the cleaved chromosomal sequence during repair ofthe double stranded break by a non-homologous repair process. Generally,donor polynucleotides comprising the targeted cleavage site(s) will becircular (e.g., can be part of a plasmid vector).

Donor Polynucleotide Comprising a Short Donor Sequence with OptionalOverhangs.

In still alternate embodiments, the donor polynucleotide can be a linearmolecule comprising a short donor sequence with optional short overhangsthat are compatible with the overhangs generated by the RNA-guidedendonuclease. In such embodiments, the donor sequence can be ligateddirectly with the cleaved chromosomal sequence during repair of thedouble-stranded break. In some instances, the donor sequence can be lessthan about 1,000, less than about 500, less than about 250, or less thanabout 100 nucleotides. In certain cases, the donor polynucleotide can bea linear molecule comprising a short donor sequence with blunt ends. Inother iterations, the donor polynucleotide can be a linear moleculecomprising a short donor sequence with 5′ and/or 3′ overhangs. Theoverhangs can comprise 1, 2, 3, 4, or 5 nucleotides.

Typically, the donor polynucleotide will be DNA. The DNA may besingle-stranded or double-stranded and/or linear or circular. The donorpolynucleotide may be a DNA plasmid, a bacterial artificial chromosome(BAC), a yeast artificial chromosome (YAC), a viral vector, a linearpiece of DNA, a PCR fragment, a naked nucleic acid, or a nucleic acidcomplexed with a delivery vehicle such as a liposome or poloxamer. Incertain embodiments, the donor polynucleotide comprising the donorsequence can be part of a plasmid vector. In any of these situations,the donor polynucleotide comprising the donor sequence can furthercomprise at least one additional sequence.

(e) Introducing into the Cell or Embryo

The RNA-targeted endonuclease(s) (or encoding nucleic acid), the guideRNA(s) (or encoding DNA), and the optional donor polynucleotide(s) canbe introduced into a cell or embryo by a variety of means. In someembodiments, the cell or embryo is transfected. Suitable transfectionmethods include calcium phosphate-mediated transfection, nucleofection(or electroporation), cationic polymer transfection (e.g., DEAE-dextranor polyethylenimine), viral transduction, virosome transfection, viriontransfection, liposome transfection, cationic liposome transfection,immunoliposome transfection, nonliposomal lipid transfection, dendrimertransfection, heat shock transfection, magnetofection, lipofection, genegun delivery, impalefection, sonoporation, optical transfection, andproprietary agent-enhanced uptake of nucleic acids. Transfection methodsare well known in the art (see, e.g., “Current Protocols in MolecularBiology” Ausubel et al., John Wiley & Sons, New York, 2003 or “MolecularCloning: A Laboratory Manual” Sambrook & Russell, Cold Spring HarborPress, Cold Spring Harbor, N.Y., 3^(rd) edition, 2001). In otherembodiments, the molecules are introduced into the cell or embryo bymicroinjection. Typically, the embryo is a fertilized one-cell stageembryo of the species of interest. For example, the molecules can beinjected into the pronuclei of one cell embryos.

The RNA-targeted endonuclease(s) (or encoding nucleic acid), the guideRNA(s) (or DNAs encoding the guide RNA), and the optional donorpolynucleotide(s) can be introduced into the cell or embryosimultaneously or sequentially. The ratio of the RNA-targetedendonuclease(s) (or encoding nucleic acid) to the guide RNA(s) (orencoding DNA) generally will be about stoichiometric such that they canform an RNA-protein complex. In one embodiment, DNA encoding anRNA-targeted endonuclease and DNA encoding a guide RNA are deliveredtogether within the plasmid vector.

(f) Culturing the Cell or Embryo

The method further comprises maintaining the cell or embryo underappropriate conditions such that the guide RNA(s) directs the RNA-guidedendonuclease(s) to the targeted site(s) in the chromosomal sequence, andthe RNA-guided endonuclease(s) introduce at least one double-strandedbreak in the chromosomal sequence. A double-stranded break can berepaired by a DNA repair process such that the chromosomal sequence ismodified by a deletion of at least one nucleotide, an insertion of atleast one nucleotide, a substitution of at least one nucleotide, or acombination thereof.

In embodiments in which no donor polynucleotide is introduced into thecell or embryo, the double-stranded break can be repaired via anon-homologous end-joining (NHEJ) repair process. Because NHEJ iserror-prone, deletions of at least one nucleotide, insertions of atleast one nucleotide, substitutions of at least one nucleotide, orcombinations thereof can occur during the repair of the break.Accordingly, the sequence at the chromosomal sequence can be modifiedsuch that the reading frame of a coding region can be shifted and thatthe chromosomal sequence is inactivated or “knocked out.” An inactivatedprotein-coding chromosomal sequence does not give rise to the proteincoded by the wild type chromosomal sequence.

In embodiments in which a donor polynucleotide comprising upstream anddownstream sequences is introduced into the cell or embryo, thedouble-stranded break can be repaired by a homology-directed repair(HDR) process such that the donor sequence is integrated into thechromosomal sequence. Accordingly, an exogenous sequence can beintegrated into the genome of the cell or embryo, or the targetedchromosomal sequence can be modified by exchange of a modified sequencefor the wild type chromosomal sequence.

In embodiments in which a donor polynucleotide comprising the targetedcleave site is introduced into the cell or embryo, the RNA-guidedendonuclease can cleave both the targeted chromosomal sequence and thedonor polynucleotide. The linearized donor polynucleotide can beintegrated into the chromosomal sequence at the site of thedouble-stranded break by ligation between the donor polynucleotide andthe cleaved chromosomal sequence via a NHEJ process.

In embodiments in which a linear donor polynucleotide comprising a shortdonor sequence is introduced into the cell or embryo, the short donorsequence can be integrated into the chromosomal sequence at the site ofthe double-stranded break via a NHEJ process. The integration canproceed via the ligation of blunt ends between the short donor sequenceand the chromosomal sequence at the site of the double stranded break.Alternatively, the integration can proceed via the ligation of stickyends (i.e., having 5′ or 3′ overhangs) between a short donor sequencethat is flanked by overhangs that are compatible with those generated bythe RNA-targeting endonuclease in the cleaved chromosomal sequence.

In general, the cell is maintained under conditions appropriate for cellgrowth and/or maintenance. Suitable cell culture conditions are wellknown in the art and are described, for example, in Santiago et al.(2008) PNAS 105:5809-5814; Moehle et al. (2007) PNAS 104:3055-3060;Urnov et al. (2005) Nature 435:646-651; and Lombardo et al (2007) Nat.Biotechnology 25:1298-1306. Those of skill in the art appreciate thatmethods for culturing cells are known in the art and can and will varydepending on the cell type. Routine optimization may be used, in allcases, to determine the best techniques for a particular cell type.

An embryo can be cultured in vitro (e.g., in cell culture). Typically,the embryo is cultured at an appropriate temperature and in appropriatemedia with the necessary O₂/CO₂ ratio to allow the expression of the RNAendonuclease and guide RNA, if necessary. Suitable non-limiting examplesof media include M2, M16, KSOM, BMOC, and HTF media. A skilled artisanwill appreciate that culture conditions can and will vary depending onthe species of embryo. Routine optimization may be used, in all cases,to determine the best culture conditions for a particular species ofembryo. In some cases, a cell line may be derived from an invitro-cultured embryo (e.g., an embryonic stem cell line).

Alternatively, an embryo may be cultured in vivo by transferring theembryo into the uterus of a female host. Generally speaking the femalehost is from the same or similar species as the embryo. Preferably, thefemale host is pseudo-pregnant. Methods of preparing pseudo-pregnantfemale hosts are known in the art. Additionally, methods of transferringan embryo into a female host are known. Culturing an embryo in vivopermits the embryo to develop and can result in a live birth of ananimal derived from the embryo. Such an animal would comprise themodified chromosomal sequence in every cell of the body.

(g) Cell and Embryo Types

A variety of eukaryotic cells and embryos are suitable for use in themethod. For example, the cell can be a human cell, a non-human mammaliancell, a non-mammalian vertebrate cell, an invertebrate cell, an insectcell, a plant cell, a yeast cell, or a single cell eukaryotic organism.In general, the embryo is non-human mammalian embryo. In specificembodiments, the embryos can be a one cell non-human mammalian embryo.Exemplary mammalian embryos, including one cell embryos, include withoutlimit mouse, rat, hamster, rodent, rabbit, feline, canine, ovine,porcine, bovine, equine, and primate embryos. In still otherembodiments, the cell can be a stem cell. Suitable stem cells includewithout limit embryonic stem cells, ES-like stem cells, fetal stemcells, adult stem cells, pluripotent stem cells, induced pluripotentstem cells, multipotent stem cells, oligopotent stem cells, unipotentstem cells and others. In exemplary embodiments, the cell is a mammaliancell.

Non-limiting examples of suitable mammalian cells include Chinesehamster ovary (CHO) cells, baby hamster kidney (BHK) cells; mousemyeloma NS0 cells, mouse embryonic fibroblast 3T3 cells (NIH3T3), mouseB lymphoma A20 cells; mouse melanoma B16 cells; mouse myoblast C2C12cells; mouse myeloma SP2/0 cells; mouse embryonic mesenchymal C3H-10T1/2cells; mouse carcinoma CT26 cells, mouse prostate DuCuP cells; mousebreast EMT6 cells; mouse hepatoma Hepa1c1c7 cells; mouse myeloma J5582cells; mouse epithelial MTD-1A cells; mouse myocardial MyEnd cells;mouse renal RenCa cells; mouse pancreatic RIN-5F cells; mouse melanomaX64 cells; mouse lymphoma YAC-1 cells; rat glioblastoma 9 L cells; rat Blymphoma RBL cells; rat neuroblastoma B35 cells; rat hepatoma cells(HTC); buffalo rat liver BRL 3A cells; canine kidney cells (MDCK);canine mammary (CMT) cells; rat osteosarcoma D17 cells; ratmonocyte/macrophage DH82 cells; monkey kidney SV-40 transformedfibroblast (COS7) cells; monkey kidney CVI-76 cells; African greenmonkey kidney (VERO-76) cells; human embryonic kidney cells (HEK293,HEK293T); human cervical carcinoma cells (HELA); human lung cells(W138); human liver cells (Hep G2); human U2-OS osteosarcoma cells,human A549 cells, human A-431 cells, and human K562 cells. An extensivelist of mammalian cell lines may be found in the American Type CultureCollection catalog (ATCC, Mamassas, Va.).

(V) Method for Using a Fusion Protein to Modify a Chromosomal Sequenceor Regulate Expression of a Chromosomal Sequence

Another aspect of the present disclosure encompasses a method formodifying a chromosomal sequence or regulating expression of achromosomal sequence in a cell or embryo. The method comprisesintroducing into the cell or embryo (a) at least one fusion protein ornucleic acid encoding at least one fusion protein, wherein the fusionprotein comprises a CRISPR/Cas-like protein or a fragment thereof and aneffector domain, and (b) at least one guide RNA or DNA encoding theguide RNA, wherein the guide RNA guides the CRISPR/Cas-like protein ofthe fusion protein to a targeted site in the chromosomal sequence andthe effector domain of the fusion protein modifies the chromosomalsequence or regulates expression of the chromosomal sequence.

Fusion proteins comprising a CRISPR/Cas-like protein or a fragmentthereof and an effector domain are detailed above in section (II). Ingeneral, the fusion proteins disclosed herein further comprise at leastone nuclear localization signal. Nucleic acids encoding fusion proteinsare described above in section (III). In some embodiments, the fusionprotein can be introduced into the cell or embryo as an isolated protein(which can further comprise a cell-penetrating domain). Furthermore, theisolated fusion protein can be part of a protein-RNA complex comprisingthe guide RNA. In other embodiments, the fusion protein can beintroduced into the cell or embryo as a RNA molecule (which can becapped and/or polyadenylated). In still other embodiments, the fusionprotein can be introduced into the cell or embryo as a DNA molecule. Forexample, the fusion protein and the guide RNA can be introduced into thecell or embryo as discrete DNA molecules or as part of the same DNAmolecule. Such DNA molecules can be plasmid vectors.

In some embodiments, the method further comprises introducing into thecell or embryo at least one zinc finger nuclease. Zinc finger nucleasesare described above in section (II)(d). In still other embodiments, themethod further comprises introducing into the cell or embryo at leastone donor polynucleotide. Donor polynucleotides are detailed above insection (IV)(d). Means for introducing molecules into cells or embryos,as well as means for culturing cell or embryos are described above insections (IV)(e) and (IV)(f), respectively. Suitable cells and embryosare described above in section (IV)(g).

In certain embodiments in which the effector domain of the fusionprotein is a cleavage domain (e.g., a FokI cleavage domain or a modifiedFokI cleavage domain), the method can comprise introducing into the cellor embryo one fusion protein (or nucleic acid encoding one fusionprotein) and two guide RNAs (or DNA encoding two guide RNAs). The twoguide RNAs direct the fusion protein to two different target sites inthe chromosomal sequence, wherein the fusion protein dimerizes (e.g.,form a homodimer) such that the two cleavage domains can introduce adouble stranded break into the chromosomal sequence. See FIG. 1A. Inembodiments in which the optional donor polynucleotide is not present,the double-stranded break in the chromosomal sequence can be repaired bya non-homologous end-joining (NHEJ) repair process. Because NHEJ iserror-prone, deletions of at least one nucleotide, insertions of atleast one nucleotide, substitutions of at least one nucleotide, orcombinations thereof can occur during the repair of the break.Accordingly, the targeted chromosomal sequence can be modified orinactivated. For example, a single nucleotide change (SNP) can give riseto an altered protein product, or a shift in the reading frame of acoding sequence can inactivate or “knock out” the sequence such that noprotein product is made. In embodiments in which the optional donorpolynucleotide is present, the donor sequence in the donorpolynucleotide can be exchanged with or integrated into the chromosomalsequence at the targeted site during repair of the double-strandedbreak. For example, in embodiments in which the donor sequence isflanked by upstream and downstream sequences having substantial sequenceidentity with upstream and downstream sequences, respectively, of thetargeted site in the chromosomal sequence, the donor sequence can beexchanged with or integrated into the chromosomal sequence at thetargeted site during repair mediated by homology-directed repairprocess. Alternatively, in embodiments in which the donor sequence isflanked by compatible overhangs (or the compatible overhangs aregenerated in situ by the RNA-guided endonuclease) the donor sequence canbe ligated directly with the cleaved chromosomal sequence by anon-homologous repair process during repair of the double-strandedbreak. Exchange or integration of the donor sequence into thechromosomal sequence modifies the targeted chromosomal sequence orintroduces an exogenous sequence into the chromosomal sequence of thecell or embryo.

In other embodiments in which the effector domain of the fusion proteinis a cleavage domain (e.g., a FokI cleavage domain or a modified FokIcleavage domain), the method can comprise introducing into the cell orembryo two different fusion proteins (or nucleic acid encoding twodifferent fusion proteins) and two guide RNAs (or DNA encoding two guideRNAs). The fusion proteins can differ as detailed above in section (II).Each guide RNA directs a fusion protein to a specific target site in thechromosomal sequence, wherein the fusion proteins dimerize (e.g., form aheterodimer) such that the two cleavage domains can introduce a doublestranded break into the chromosomal sequence. In embodiments in whichthe optional donor polynucleotide is not present, the resultantdouble-stranded breaks can be repaired by a non-homologous repairprocess such that deletions of at least one nucleotide, insertions of atleast one nucleotide, substitutions of at least one nucleotide, orcombinations thereof can occur during the repair of the break. Inembodiments in which the optional donor polynucleotide is present, thedonor sequence in the donor polynucleotide can be exchanged with orintegrated into the chromosomal sequence during repair of thedouble-stranded break by either a homology-based repair process (e.g.,in embodiments in which the donor sequence is flanked by upstream anddownstream sequences having substantial sequence identity with upstreamand downstream sequences, respectively, of the targeted sites in thechromosomal sequence) or a non-homologous repair process (e.g., inembodiments in which the donor sequence is flanked by compatibleoverhangs).

In still other embodiments in which the effector domain of the fusionprotein is a cleavage domain (e.g., a FokI cleavage domain or a modifiedFokI cleavage domain), the method can comprise introducing into the cellor embryo one fusion protein (or nucleic acid encoding one fusionprotein), one guide RNA (or DNA encoding one guide RNA), and one zincfinger nuclease (or nucleic acid encoding the zinc finger nuclease),wherein the zinc finger nuclease comprises a FokI cleavage domain or amodified FokI cleavage domain. The guide RNA directs the fusion proteinto a specific chromosomal sequence, and the zinc finger nuclease isdirected to another chromosomal sequence, wherein the fusion protein andthe zinc finger nuclease dimerize such that the cleavage domain of thefusion protein and the cleavage domain of the zinc finger nuclease canintroduce a double stranded break into the chromosomal sequence. SeeFIG. 1B. In embodiments in which the optional donor polynucleotide isnot present, the resultant double-stranded breaks can be repaired by anon-homologous repair process such that deletions of at least onenucleotide, insertions of at least one nucleotide, substitutions of atleast one nucleotide, or combinations thereof can occur during therepair of the break. In embodiments in which the optional donorpolynucleotide is present, the donor sequence in the donorpolynucleotide can be exchanged with or integrated into the chromosomalsequence during repair of the double-stranded break by either ahomology-based repair process (e.g., in embodiments in which the donorsequence is flanked by upstream and downstream sequences havingsubstantial sequence identity with upstream and downstream sequences,respectively, of the targeted sites in the chromosomal sequence) or anon-homologous repair process (e.g., in embodiments in which the donorsequence is flanked by compatible overhangs).

In still other embodiments in which the effector domain of the fusionprotein is a transcriptional activation domain or a transcriptionalrepressor domain, the method can comprise introducing into the cell orembryo one fusion protein (or nucleic acid encoding one fusion protein)and one guide RNA (or DNA encoding one guide RNA). The guide RNA directsthe fusion protein to a specific chromosomal sequence, wherein thetranscriptional activation domain or a transcriptional repressor domainactivates or represses expression, respectively, of the targetedchromosomal sequence. See FIG. 2A.

In alternate embodiments in which the effector domain of the fusionprotein is an epigenetic modification domain, the method can compriseintroducing into the cell or embryo one fusion protein (or nucleic acidencoding one fusion protein) and one guide RNA (or DNA encoding oneguide RNA). The guide RNA directs the fusion protein to a specificchromosomal sequence, wherein the epigenetic modification domainmodifies the structure of the targeted the chromosomal sequence. SeeFIG. 2A. Epigenetic modifications include acetylation, methylation ofhistone proteins and/or nucleotide methylation. In some instances,structural modification of the chromosomal sequence leads to changes inexpression of the chromosomal sequence.

(VI) Genetically Modified Cells and Animals

The present disclosure encompasses genetically modified cells, non-humanembryos, and non-human animals comprising at least one chromosomalsequence that has been modified using an RNA-guidedendonuclease-mediated or fusion protein-mediated process, for example,using the methods described herein. The disclosure provides cellscomprising at least one DNA or RNA molecule encoding an RNA-guidedendonuclease or fusion protein targeted to a chromosomal sequence ofinterest or a fusion protein, at least one guide RNA, and optionally oneor more donor polynucleotide(s). The disclosure also provides non-humanembryos comprising at least one DNA or RNA molecule encoding anRNA-guided endonuclease or fusion protein targeted to a chromosomalsequence of interest, at least one guide RNA, and optionally one or moredonor polynucleotide(s).

The present disclosure provides genetically modified non-human animals,non-human embryos, or animal cells comprising at least one modifiedchromosomal sequence. The modified chromosomal sequence may be modifiedsuch that it is (1) inactivated, (2) has an altered expression orproduces an altered protein product, or (3) comprises an integratedsequence. The chromosomal sequence is modified with an RNA guidedendonuclease-mediated or fusion protein-mediated process, using themethods described herein.

As discussed, one aspect of the present disclosure provides agenetically modified animal in which at least one chromosomal sequencehas been modified. In one embodiment, the genetically modified animalcomprises at least one inactivated chromosomal sequence. The modifiedchromosomal sequence may be inactivated such that the sequence is nottranscribed and/or a functional protein product is not produced. Thus, agenetically modified animal comprising an inactivated chromosomalsequence may be termed a “knock out” or a “conditional knock out.” Theinactivated chromosomal sequence can include a deletion mutation (i.e.,deletion of one or more nucleotides), an insertion mutation (i.e.,insertion of one or more nucleotides), or a nonsense mutation (i.e.,substitution of a single nucleotide for another nucleotide such that astop codon is introduced). As a consequence of the mutation, thetargeted chromosomal sequence is inactivated and a functional protein isnot produced. The inactivated chromosomal sequence comprises noexogenously introduced sequence. Also included herein are geneticallymodified animals in which two, three, four, five, six, seven, eight,nine, or ten or more chromosomal sequences are inactivated.

In another embodiment, the modified chromosomal sequence can be alteredsuch that it codes for a variant protein product. For example, agenetically modified animal comprising a modified chromosomal sequencecan comprise a targeted point mutation(s) or other modification suchthat an altered protein product is produced. In one embodiment, thechromosomal sequence can be modified such that at least one nucleotideis changed and the expressed protein comprises one changed amino acidresidue (missense mutation). In another embodiment, the chromosomalsequence can be modified to comprise more than one missense mutationsuch that more than one amino acid is changed. Additionally, thechromosomal sequence can be modified to have a three nucleotide deletionor insertion such that the expressed protein comprises a single aminoacid deletion or insertion. The altered or variant protein can havealtered properties or activities compared to the wild type protein, suchas altered substrate specificity, altered enzyme activity, alteredkinetic rates, etc.

In another embodiment, the genetically modified animal can comprise atleast one chromosomally integrated sequence. A genetically modifiedanimal comprising an integrated sequence may be termed a “knock in” or a“conditional knock in.” The chromosomally integrated sequence can, forexample, encode an orthologous protein, an endogenous protein, orcombinations of both. In one embodiment, a sequence encoding anorthologous protein or an endogenous protein can be integrated into achromosomal sequence encoding a protein such that the chromosomalsequence is inactivated, but the exogenous sequence is expressed. Insuch a case, the sequence encoding the orthologous protein or endogenousprotein may be operably linked to a promoter control sequence.Alternatively, a sequence encoding an orthologous protein or anendogenous protein may be integrated into a chromosomal sequence withoutaffecting expression of a chromosomal sequence. For example, a sequenceencoding a protein can be integrated into a “safe harbor” locus, such asthe Rosa26 locus, HPRT locus, or AAV locus. The present disclosure alsoencompasses genetically modified animals in which two, three, four,five, six, seven, eight, nine, or ten or more sequences, includingsequences encoding protein(s), are integrated into the genome.

The chromosomally integrated sequence encoding a protein can encode thewild type form of a protein of interest or can encode a proteincomprising at least one modification such that an altered version of theprotein is produced. For example, a chromosomally integrated sequenceencoding a protein related to a disease or disorder can comprise atleast one modification such that the altered version of the proteinproduced causes or potentiates the associated disorder. Alternatively,the chromosomally integrated sequence encoding a protein related to adisease or disorder can comprise at least one modification such that thealtered version of the protein protects against the development of theassociated disorder.

In an additional embodiment, the genetically modified animal can be a“humanized” animal comprising at least one chromosomally integratedsequence encoding a functional human protein. The functional humanprotein can have no corresponding ortholog in the genetically modifiedanimal. Alternatively, the wild type animal from which the geneticallymodified animal is derived may comprise an ortholog corresponding to thefunctional human protein. In this case, the orthologous sequence in the“humanized” animal is inactivated such that no functional protein ismade and the “humanized” animal comprises at least one chromosomallyintegrated sequence encoding the human protein.

In yet another embodiment, the genetically modified animal can compriseat least one modified chromosomal sequence encoding a protein such thatthe expression pattern of the protein is altered. For example,regulatory regions controlling the expression of the protein, such as apromoter or a transcription factor binding site, can be altered suchthat the protein is over-produced, or the tissue-specific or temporalexpression of the protein is altered, or a combination thereof.Alternatively, the expression pattern of the protein can be alteredusing a conditional knockout system. A non-limiting example of aconditional knockout system includes a Cre-lox recombination system. ACre-lox recombination system comprises a Cre recombinase enzyme, asite-specific DNA recombinase that can catalyze the recombination of anucleic acid sequence between specific sites (lox sites) in a nucleicacid molecule. Methods of using this system to produce temporal andtissue specific expression are known in the art. In general, agenetically modified animal is generated with lox sites flanking achromosomal sequence. The genetically modified animal comprising thelox-flanked chromosomal sequence can then be crossed with anothergenetically modified animal expressing Cre recombinase. Progeny animalscomprising the lox-flanked chromosomal sequence and the Cre recombinaseare then produced, and the lox-flanked chromosomal sequence isrecombined, leading to deletion or inversion of the chromosomal sequenceencoding the protein. Expression of Cre recombinase can be temporallyand conditionally regulated to effect temporally and conditionallyregulated recombination of the chromosomal sequence.

In any of these embodiments, the genetically modified animal disclosedherein can be heterozygous for the modified chromosomal sequence.Alternatively, the genetically modified animal can be homozygous for themodified chromosomal sequence.

The genetically modified animals disclosed herein can be crossbred tocreate animals comprising more than one modified chromosomal sequence orto create animals that are homozygous for one or more modifiedchromosomal sequences. For example, two animals comprising the samemodified chromosomal sequence can be crossbred to create an animalhomozygous for the modified chromosomal sequence. Alternatively, animalswith different modified chromosomal sequences can be crossbred to createan animal comprising both modified chromosomal sequences.

For example, a first animal comprising an inactivated chromosomalsequence gene “x” can be crossed with a second animal comprising achromosomally integrated sequence encoding a human gene “X” protein togive rise to “humanized” gene “X” offspring comprising both theinactivated gene “x” chromosomal sequence and the chromosomallyintegrated human gene “X” sequence. Also, a humanized gene “X” animalcan be crossed with a humanized gene “Y” animal to create humanized geneX/gene Y offspring. Those of skill in the art will appreciate that manycombinations are possible.

In other embodiments, an animal comprising a modified chromosomalsequence can be crossbred to combine the modified chromosomal sequencewith other genetic backgrounds. By way of non-limiting example, othergenetic backgrounds may include wild-type genetic backgrounds, geneticbackgrounds with deletion mutations, genetic backgrounds with anothertargeted integration, and genetic backgrounds with non-targetedintegrations.

The term “animal,” as used herein, refers to a non-human animal. Theanimal may be an embryo, a juvenile, or an adult. Suitable animalsinclude vertebrates such as mammals, birds, reptiles, amphibians,shellfish, and fish. Examples of suitable mammals include without limitrodents, companion animals, livestock, and primates. Non-limitingexamples of rodents include mice, rats, hamsters, gerbils, and guineapigs. Suitable companion animals include but are not limited to cats,dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples oflivestock include horses, goats, sheep, swine, cattle, llamas, andalpacas. Suitable primates include but are not limited to capuchinmonkeys, chimpanzees, lemurs, macaques, marmosets, tamarins, spidermonkeys, squirrel monkeys, and vervet monkeys. Non-limiting examples ofbirds include chickens, turkeys, ducks, and geese. Alternatively, theanimal may be an invertebrate such as an insect, a nematode, and thelike. Non-limiting examples of insects include Drosophila andmosquitoes. An exemplary animal is a rat. Non-limiting examples ofsuitable rat strains include Dahl Salt-Sensitive, Fischer 344, Lewis,Long Evans Hooded, Sprague-Dawley, and Wistar. In one embodiment, theanimal is not a genetically modified mouse. In each of the foregoingiterations of suitable animals for the invention, the animal does notinclude exogenously introduced, randomly integrated transposonsequences.

A further aspect of the present disclosure provides genetically modifiedcells or cell lines comprising at least one modified chromosomalsequence. The genetically modified cell or cell line can be derived fromany of the genetically modified animals disclosed herein. Alternatively,the chromosomal sequence can be modified in a cell as described hereinabove (in the paragraphs describing chromosomal sequence modificationsin animals) using the methods descried herein. The disclosure alsoencompasses a lysate of said cells or cell lines.

In general, the cells are eukaryotic cells. Suitable host cells includefungi or yeast, such as Pichia, Saccharomyces, or Schizosaccharomyces;insect cells, such as SF9 cells from Spodoptera frugiperda or S2 cellsfrom Drosophila melanogaster; and animal cells, such as mouse, rat,hamster, non-human primate, or human cells. Exemplary cells aremammalian. The mammalian cells can be primary cells. In general, anyprimary cell that is sensitive to double strand breaks may be used. Thecells may be of a variety of cell types, e.g., fibroblast, myoblast, Tor B cell, macrophage, epithelial cell, and so forth.

When mammalian cell lines are used, the cell line can be any establishedcell line or a primary cell line that is not yet described. The cellline can be adherent or non-adherent, or the cell line can be grownunder conditions that encourage adherent, non-adherent or organotypicgrowth using standard techniques known to individuals skilled in theart. Non-limiting examples of suitable mammalian cells and cell linesare provided herein in section (IV)(g). In still other embodiments, thecell can be a stem cell. Non-limiting examples of suitable stem cellsare provided in section (IV)(g).

The present disclosure also provides a genetically modified non-humanembryo comprising at least one modified chromosomal sequence. Thechromosomal sequence can be modified in an embryo as described hereinabove (in the paragraphs describing chromosomal sequence modificationsin animals) using the methods descried herein. In one embodiment, theembryo is a non-human fertilized one-cell stage embryo of the animalspecies of interest. Exemplary mammalian embryos, including one cellembryos, include without limit, mouse, rat, hamster, rodent, rabbit,feline, canine, ovine, porcine, bovine, equine, and primate embryos.

DEFINITIONS

Unless defined otherwise, all technical and scientific terms used hereinhave the meaning commonly understood by a person skilled in the art towhich this invention belongs. The following references provide one ofskill with a general definition of many of the terms used in thisinvention: Singleton et al., Dictionary of Microbiology and MolecularBiology (2nd ed. 1994); The Cambridge Dictionary of Science andTechnology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R.Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, TheHarper Collins Dictionary of Biology (1991). As used herein, thefollowing terms have the meanings ascribed to them unless specifiedotherwise.

When introducing elements of the present disclosure or the preferredembodiments(s) thereof, the articles “a”, “an”, “the” and “said” areintended to mean that there are one or more of the elements. The terms“comprising”, “including” and “having” are intended to be inclusive andmean that there may be additional elements other than the listedelements.

As used herein, the term “endogenous sequence” refers to a chromosomalsequence that is native to the cell.

The term “exogenous,” as used herein, refers to a sequence that is notnative to the cell, or a chromosomal sequence whose native location inthe genome of the cell is in a different chromosomal location.

A “gene,” as used herein, refers to a DNA region (including exons andintrons) encoding a gene product, as well as all DNA regions whichregulate the production of the gene product, whether or not suchregulatory sequences are adjacent to coding and/or transcribedsequences. Accordingly, a gene includes, but is not necessarily limitedto, promoter sequences, terminators, translational regulatory sequencessuch as ribosome binding sites and internal ribosome entry sites,enhancers, silencers, insulators, boundary elements, replicationorigins, matrix attachment sites, and locus control regions.

The term “heterologous” refers to an entity that is not endogenous ornative to the cell of interest. For example, a heterologous proteinrefers to a protein that is derived from or was originally derived froman exogenous source, such as an exogenously introduced nucleic acidsequence. In some instances, the heterologous protein is not normallyproduced by the cell of interest.

The terms “nucleic acid” and “polynucleotide” refer to adeoxyribonucleotide or ribonucleotide polymer, in linear or circularconformation, and in either single- or double-stranded form. For thepurposes of the present disclosure, these terms are not to be construedas limiting with respect to the length of a polymer. The terms canencompass known analogs of natural nucleotides, as well as nucleotidesthat are modified in the base, sugar and/or phosphate moieties (e.g.,phosphorothioate backbones). In general, an analog of a particularnucleotide has the same base-pairing specificity; i.e., an analog of Awill base-pair with T.

The term “nucleotide” refers to deoxyribonucleotides or ribonucleotides.The nucleotides may be standard nucleotides (i.e., adenosine, guanosine,cytidine, thymidine, and uridine) or nucleotide analogs. A nucleotideanalog refers to a nucleotide having a modified purine or pyrimidinebase or a modified ribose moiety. A nucleotide analog may be a naturallyoccurring nucleotide (e.g., inosine) or a non-naturally occurringnucleotide. Non-limiting examples of modifications on the sugar or basemoieties of a nucleotide include the addition (or removal) of acetylgroups, amino groups, carboxyl groups, carboxymethyl groups, hydroxylgroups, methyl groups, phosphoryl groups, and thiol groups, as well asthe substitution of the carbon and nitrogen atoms of the bases withother atoms (e.g., 7-deaza purines). Nucleotide analogs also includedideoxy nucleotides, 2′-O-methyl nucleotides, locked nucleic acids(LNA), peptide nucleic acids (PNA), and morpholinos.

The terms “polypeptide” and “protein” are used interchangeably to referto a polymer of amino acid residues.

Techniques for determining nucleic acid and amino acid sequence identityare known in the art. Typically, such techniques include determining thenucleotide sequence of the mRNA for a gene and/or determining the aminoacid sequence encoded thereby, and comparing these sequences to a secondnucleotide or amino acid sequence. Genomic sequences can also bedetermined and compared in this fashion. In general, identity refers toan exact nucleotide-to-nucleotide or amino acid-to-amino acidcorrespondence of two polynucleotides or polypeptide sequences,respectively. Two or more sequences (polynucleotide or amino acid) canbe compared by determining their percent identity. The percent identityof two sequences, whether nucleic acid or amino acid sequences, is thenumber of exact matches between two aligned sequences divided by thelength of the shorter sequences and multiplied by 100. An approximatealignment for nucleic acid sequences is provided by the local homologyalgorithm of Smith and Waterman, Advances in Applied Mathematics2:482-489 (1981). This algorithm can be applied to amino acid sequencesby using the scoring matrix developed by Dayhoff, Atlas of ProteinSequences and Structure, M. O. Dayhoff ed., 5 suppl. 3:353-358, NationalBiomedical Research Foundation, Washington, D.C., USA, and normalized byGribskov, Nucl. Acids Res. 14(6):6745-6763 (1986). An exemplaryimplementation of this algorithm to determine percent identity of asequence is provided by the Genetics Computer Group (Madison, Wis.) inthe “BestFit” utility application. Other suitable programs forcalculating the percent identity or similarity between sequences aregenerally known in the art, for example, another alignment program isBLAST, used with default parameters. For example, BLASTN and BLASTP canbe used using the following default parameters: genetic code=standard;filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62;Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant,GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+Swissprotein+Spupdate+PIR. Details of these programs can be found on theGenBank website.

As various changes could be made in the above-described cells andmethods without departing from the scope of the invention, it isintended that all matter contained in the above description and in theexamples given below, shall be interpreted as illustrative and not in alimiting sense.

EXAMPLES

The following examples illustrate certain aspects of the invention.

Example 1 Modification of Cas9 Gene for Mammalian Expression

A Cas9 gene from Streptococcus pyogenes strain MGAS15252 (Accessionnumber YP_(—)005388840.1) was optimized with Homo sapiens codonpreference to enhance its translation in mammalian cells. The Cas9 genealso was modified by adding a nuclear localization signal PKKKRKV (SEQID NO:1) at the C terminus for targeting the protein into the nuclei ofmammalian cells. Table 1 presents the modified Cas9 amino acid sequence,with the nuclear localization sequence underlined. Table 2 presents thecodon optimized, modified Cas9 DNA sequence.

TABLE 1 Modified Cas9 Amino Acid SequenceMDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGALLFGSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLADSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQIYNQLFEENPINASRVDAKAILSARLSKSRRLENLIAQLPGEKRNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNSEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGAYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDRGMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGHSLHEQIANLAGSPAIKKGILQTVKIVDELVKVMGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFIKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEGKQLFVEQHKHYLDEIIEGISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDPKKKRKV (SEQ ID NO:9)

TABLE 2 Optimized Cas9 DNA Sequence (5′-3′)ATGGACAAGAAGTACAGCATCGGCCTGGACATCGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGACTACAAGGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACCGACCGGCACAGCATCAAGAAGAACCTGATCGGCGCCCTGCTGTTCGGCTCTGGCGAAACAGCCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCAGACGGAAGAACCGGATCTGCTATCTGCAAGAGATCTTCAGCAACGAGATGGCCAAGGTGGACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAAGAGGATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGAGGTGGCCTACCACGAGAAGTACCCCACCATCTACCACCTGAGAAAGAAGCTGGCCGACAGCACCGACAAGGCCGACCTGAGACTGATCTACCTGGCCCTGGCCCACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAACCCCGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTGCAGATCTACAATCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCAGAGTGGACGCCAAGGCCATCCTGAGCGCCAGACTGAGCAAGAGCAGACGGCTGGAAAATCTGATCGCCCAGCTGCCCGGCGAGAAGCGGAATGGCCTGTTCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCGACCTGGCCGAGGATGCCAAACTGCAGCTGAGCAAGGACACCTACGACGACGACCTGGACAACCTGCTGGCCCAGATCGGCGACCAGTACGCCGACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGAACAGCGAGATCACCAAGGCCCCCCTGTCCGCCTCTATGATCAAGAGATACGACGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTCGTGCGGCAGCAGCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAAGAACGGCTACGCCGGCTACATCGATGGCGGAGCCAGCCAGGAAGAGTTCTACAAGTTCATCAAGCCCATCCTGGAAAAGATGGACGGCACCGAGGAACTGCTCGTGAAGCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACAACGGCAGCATCCCCCACCAGATCCACCTGGGAGAGCTGCACGCCATTCTGCGGCGGCAGGAAGATTTTTACCCATTCCTGAAGGACAACCGGGAAAAGATCGAGAAGATCCTGACCTTCAGAATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAAACAGCAGATTCGCCTGGATGACCAGAAAGAGCGAGGAAACCATCACCCCCTGGAACTTCGAGGAAGTGGTGGACAAGGGCGCCAGCGCCCAGAGCTTCATCGAGCGGATGACCAACTTCGATAAGAACCTGCCCAACGAGAAGGTGCTGCCCAAGCACAGCCTGCTGTACGAGTACTTCACCGTGTACAACGAGCTGACCAAAGTGAAATACGTGACCGAGGGAATGCGGAAGCCCGCCTTTCTGAGCGGCGAGCAGAAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTGAAAGAGGACTACTTCAAGAAAATCGAGTGCTTCGACAGCGTGGAAATCAGCGGCGTGGAAGATCGGTTCAACGCCTCCCTGGGCGCCTATCACGATCTGCTGAAAATTATCAAGGACAAGGACTTCCTGGACAATGAGGAAAACGAGGACATTCTGGAAGATATCGTGCTGACCCTGACACTGTTTGAGGACCGGGGCATGATCGAGGAACGGCTGAAAACCTATGCCCACCTGTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATACACCGGCTGGGGCAGGCTGAGCCGGAAGCTGATCAACGGCATCCGGGACAAGCAGTCCGGCAAGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGAAACTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGGACATCCAGAAAGCCCAGGTGTCCGGCCAGGGACACTCTCTGCACGAGCAGATCGCCAATCTGGCCGGATCCCCCGCCATTAAGAAGGGCATCCTGCAGACAGTGAAGATTGTGGACGAGCTCGTGAAAGTGATGGGCCACAAGCCCGAGAACATCGTGATCGAAATGGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAGAACAGCCGCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGGCAGCCAGATCCTGAAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACGAGAAGCTGTACCTGTACTACCTGCAGAATGGGCGGGATATGTACGTGGACCAGGAACTGGACATCAACCGGCTGTCCGACTACGATGTGGACCACATTGTGCCCCAGTCCTTCATCAAGGACGACTCCATCGATAACAAAGTGCTGACTCGGAGCGACAAGAACCGGGGCAAGAGCGACAACGTGCCCTCCGAAGAGGTCGTGAAGAAGATGAAGAACTACTGGCGCCAGCTGCTGAATGCCAAGCTGATTACCCAGAGGAAGTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCCGGCTTCATTAAGCGGCAGCTGGTGGAAACCCGGCAGATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACACTAAGTACGACGAGAACGACAAACTGATCCGGGAAGTGAAAGTGATCACCCTGAAGTCCAAGCTGGTGTCCGACTTCAGAAAGGATTTCCAGTTTTACAAAGTGCGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCCGTCGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTTCGTGTACGGCGATTACAAGGTGTACGACGTGCGGAAGATGATCGCCAAGAGCGAGCAGGAAATCGGCAAGGCTACCGCCAAGTACTTCTTCTACAGCAACATCATGAACTTTTTCAAGACCGAGATCACACTGGCCAACGGCGAGATCAGAAAGCGGCCTCTGATCGAGACAAACGGCGAAACCGGGGAGATCGTGTGGGATAAGGGCCGGGATTTTGCCACAGTGCGGAAAGTGCTGTCCATGCCCCAAGTGAATATCGTGAAAAAGACCGAGGTGCAGACCGGCGGCTTCAGCAAAGAGTCTATCCTGCCCAAGAGGAACTCCGACAAGCTGATCGCCAGAAAGAAGGATTGGGACCCTAAGAAGTACGGCGGCTTTGACAGCCCCACCGTGGCCTACTCTGTGCTGGTGGTGGCCAAAGTGGAAAAGGGCAAGTCCAAGAAACTGAAGAGTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGAAGCAGCTTCGAGAAGAATCCCATCGACTTTCTGGAAGCCAAGGGCTACAAAGAAGTGAAAAAGGACCTGATCATCAAGCTGCCTAAGTACTCCCTGTTCGAGCTGGAAAACGGCCGGAAGCGGATGCTGGCTTCTGCCGGCGAACTGCAGAAGGGAAACGAGCTGGCCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGGCCAGCCACTATGAGAAGCTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACAGCTGTTTGTGGAACAGCACAAGCACTACCTGGACGAGATCATCGAGCAGATTAGCGAGTTCTCCAAGCGCGTGATCCTGGCCGATGCCAACCTGGACAAGGTGCTGAGCGCCTACAACAAGCACCGGGATAAGCCCATCAGAGAGCAGGCCGAGAATATCATCCACCTGTTTACCCTGACCAACCTGGGAGCCCCTGCCGCCTTCAAGTACTTTGACACCACCATCGACCGGAAGAGGTACACCAGCACCAAAGAGGTGCTGGACGCCACCCTGATCCACCAGAGCATCACCGGCCTGTACGAGACACGGATCGACCTGTCTCAGCTGGGAGGCGACCCCAAGAAAAAGCGCAAAGTG (SEQ ID NO: 10)

The modified Cas9 DNA sequence was placed under the control ofcytomegalovirus (CMV) promoter for constituent expression in mammaliancells. The modified Cas9 DNA sequence was also placed under the controlT7 promoter for in vitro mRNA synthesis with T7 RNA polymerase. In vitroRNA transcription was performed by using MessageMAX T7 ARCA-CappedMessage Transcription Kit and T7 mScript Standard mRNA Production System(Cellscript).

Example 2 Targeting Cas9

The adeno-associated virus integration site 1 (AAVS1) locus was used asa target for Cas9-mediated human genome modification. The human AAVS1locus is located in intron 1 (4427 bp) of protein phosphatase 1,regulatory subunit 12C (PPP1R12C). Table 3 presents the first exon(shaded gray) and the first intron of PPP1R12C. The underlined sequencewithin the intron is the targeted modification site (i.e., AAVS1 locus).

TABLE 3 First Exon and Intron of PPP1R12C (5'-3')

GCCCGGCGTCTCCCGGGGCCAGGTCCACCCTCTGCTGCGCCACCTGGGGCATCCTCCTTCCCCGTTGCCAGTCTCGATCCGCCCCGTCGTTCCTGGCCCTGGGCTTTGCCACCCTATGCTGACACCCCGTCCCAGTCCCCCTTACCATTCCCCTTCGACCACCCCACTTCCGAATTGGAGCCGCTTCAACTGGCCCTGGGCTTAGCCACTCTGTGCTGACCACTCTGCCCCAGGCCTCCTTACCATTCCCCTTCGACCTACTCTCTTCCGCATTGGAGTCGCTTTAACTGGCCCTGGCTTTGGCAGCCTGTGCTGACCCATGCAGTCCTCCTTACCATCCCTCCCTCGACTTCCCCTCTTCCGATGTTGAGCCCCTCCAGCCGGTCCTGGACTTTGTCTCCTTCCCTGCCCTGCCCTCTCCTGAACCTGAGCCAGCTCCCATAGCTCAGTCTGGTCTATCTGCCTGGCCCTGGCCATTGTCACTTTGCGCTGCCCTCCTCTCGCCCCCGAGTGCCCTTGCTGTGCCGCCGGAACTCTGCCCTCTAACGCTGCCGTCTCTCTCCTGAGTCCGGACCACTTTGAGCTCTACTGGCTTCTGCGCCGCCTCTGGCCCACTGTTTCCCCTTCCCAGGCAGGTCCTGCTTTCTCTGACCTGCATTCTCTCCCCTGGGCCTGTGCCGCTTTCTGTCTGCAGCTTGTGGCCTGGGTCACCTCTACGGCTGGCCCAGATCCTTCCCTGCCGCCTCCTTCAGGTTCCGTCTTCCTCCACTCCCTCTTCCCCTTGCTCTCTGCTGTGTTGCTGCCCAAGGATGCTCTTTCCGGAGCACTTCCTTCTCGGCGCTGCACCACGTGATGTCCTCTGAGCGGATCCTCCCCGTGTCTGGGTCCTCTCCGGGCATCTCTCCTCCCTCACCCAACCCCATGCCGTCTTCACTCGCTGGGTTCCCTTTTCCTTCTCCTTCTGGGGCCTGTGCCATCTCTCGTTTCTTAGGATGGCCTTCTCCGACGGATGTCTCCCTTGCGTCCCGCCTCCCCTTCTTGTAGGCCTGCATCATCACCGTTTTTCTGGACAACCCCAAAGTACCCCGTCTCCCTGGCTTTAGCCACCTCTCCATCCTCTTGCTTTCTTTGCCTGGACACCCCGTTCTCCTGTGGATTCGGGTCACCTCTCACTCCTTTCATTTGGGCAGCTCCCCTACCCCCCTTACCTCTCTAGTCTGTGCTAGCTCTTCCAGCCCCCTGTCATGGCATCTTCCAGGGGTCCGAGAGCTCAGCTAGTCTTCTTCCTCCAACCCGGGCCCCTATGTCCACTTCAGGACAGCATGTTTGCTGCCTCCAGGGATCCTGTGTCCCCGAGCTGGGACCACCTTATATTCCCAGGGCCGGTTAATGTGGCTCTGGTTCTGGGTACTTTTATCTGTCCCCTCCACCCCACAGTGGGGCCACTAGGGACAGGATTGGTGACAGAAAAGCCCCATCCTTAGGCCTCCTCCTTCCTAGTCTCCTGATATTGGGTCTAACCCCCACCTCCTGTTAGGCAGATTCCTTATCTGGTGACACACCCCCATTTCCTGGAGCCATCTCTCTCCTTGCCAGAACCTCTAAGGTTTGCTTACGATGGAGCCAGAGAGGATCCTGGGAGGGAGAGCTTGGCAGGGGGTGGGAGGGAAGGGGGGGATGCGTGACCTGCCCGGTTCTCAGTGGCCACCCTGCGCTACCCTCTCCCAGAACCTGAGCTGCTCTGACGCGGCCGTCTGGTGCGTTTCACTGATCCTGGTGCTGCAGCTTCCTTACACTTCCCAAGAGGAGAAGCAGTTTGGAAAAACAAAATCAGAATAAGTTGGTCCTGAGTTCTAACTTTGGCTCTTCACCTTTCTAGTCCCCAATTTATATTGTTCCTCCGTGCGTCAGTTTTACCTGTGAGATAAGGCCAGTAGCCAGCCCCGTCCTGGCAGGGCTGTGGTGAGGAGGGGGGTGTCCGTGTGGAAAACTCCCTTTGTGAGAATGGTGCGTCCTAGGTGTTCACCAGGTCGTGGCCGCCTCTACTCCCTTTCTCTTTCTCCATCCTTCTTTCCTTAAAGAGTCCCCAGTGCTATCTGGGACATATTCCTCCGCCCAGAGCAGGGTCCCGCTTCCCTAAGGCCCTGCTCTGGGCTTCTGGGTTTGAGTCCTTGGCAAGCCCAGGAGAGGCGCTCAGGCTTCCCTGTCCCCCTTCCTCGTCCACCATCTCATGCCCCTGGCTCTCCTGCCCCTTCCCTACAGGGGTTCCTGGCTCTGCTCTTCAGACTGAGCCCCGTTCCCCTGCATCCCCGTTCCCCTGCATCCCCCTTCCCCTGCATCCCCCAGAGGCCCCAGGCCACCTACTTGGCCTGGACCCCACGAGAGGCCACCCCAGCCCTGTCTACCAGGCTGCCTTTTGGGTGGATTCTCCTCCAACTGTGGGGTGACTGCTTGGCAAACTCACTCTTCGGGGTATCCCAGGAGGCCTGGAGCATTGGGGTGGGCTGGGGTTCAGAGAGGAGGGATTCCCTTCTCAGGTTACGTGGCCAAGAAGCAGGGGAGCTGGGTTTGGGTCAGGTCTGGGTGTGGGGTGACCAGCTTATGCTGTTTGCCCAGGACAGCCTAGTTTTAGCACTGAAACCCTCAGTCCTAGGAAAACAGGGATGGTTGGTCACTGTCTCTGGGTGACTCTTGATTCCCGGCCAGTTTCTCCACCTGGGGCTGTGTTTCTCGTCCTGCATCCTTCTCCAGGCAGGTCCCCAAGCATCGCCCCCCTGCTGTGGCTGTTCCCAAGTTCTTAGGGTACCCCACGTGGGTTTATCAACCACTTGGTGAGGCTGGTACCCTGCCCCCATTCCTGCACCCCAATTGCCTTAGTGGCTAGGGGGTTGGGGGCTAGAGTAGGAGGGGCTGGAGCCAGGATTCTTAGGGCTGAACAGAGAAGAGCTGGGGGCCTGGGCTCCTGGGTTTGAGAGAGGAGGGGCTGGGGCCTGGACTCCTGGGTCCGAGGGAGGAGGGGCTGGGGCCTGGACTCCTGGGTCTGAGGGTGGAGGGACTGGGGGCCTGGACTCCTGGGTCCGAGGGAGGAGGGGCTGGGGCCTGGACTCGTGGGTCTGAGGGAGGAGGGGCTGGGGGCCTGGACTTCTGGGTCTTAGGGAGGCGGGGCTGGGCCTGGACCCCTGGGTCTGAATGGGGAGAGGCTGGGGGCCTGGACTCCTTCATCTGAGGGCGGAAGGGCTGGGGCCTGGCCTCCTGGGTTGAATGGGGAGGGGTTGGGCCTGGACTCTGGAGTCCCTGGTGCCCAGGCCTCAGGCATCTTTCACAGGGATGCCTGTACTGGGCAGGTCCTTGAAAGGGAAAGGCCCATTGCTCTCCTTGCCCCCCTCCCCTATCGCCATGACAACTGGGTGGAAATAAACGAGCCGAGTTCATCCCGTTCCCAGGGCACGTGCGGCCCCTTCACAGCCCGAGTTTCCATGACCTCATGCTCTTGGCCCTCGTAGCTCCCTCCCGCCTCCTCCAGATGGGCAGCTTTGGAGAGGTGAGGGACTTGGGGGGTAATTTATCCCGTGGATCTAGGAGTTTAGCTTCACTCCTTCCTCAGCTCCAGTTCAGGTCCCGGAGCCCACCCAGTGTCCACAAGGCCTGGGGCAAGTCCCTCCTCCGACCCCCTGGACTTCGGCTTTTGTCCCCCCAAGTTTTGGACCCCTAAGGGAAGAATGAGAAACGGTGGCCCGTGTCAGCCCCTGGCTGCAGGGCCCCGTGCAGAGGGGGCCTCAGTGAACTGGAGTGTGACAGCCTGGGGCCCAGGCACACAGGTGTGCAGCTGTCTCACCCCTCTGGGAGTCCCGCCCAGGCCCCTGAGTCTGTCCCAGCACAGGGTGGCCTTCCTCCACCCTGCATAGCCCTGGGCCCACGGCTTCGTTCCTGCAGAGTATCTGCTGGGGTGGTTTCCGAGCTTGACCCTTGGAAGGACCTGGCTGGGTTTAAGGCAGGAGGGGCTGGGGGCCAGGACTCCTGGCTCTGAAGGAGGAGGGGCTGGAACCTCTTCCCTAGTCTGAGCACTGGAAGCGCCACCTGTGGGTGGTGACGGGGGTTTTGCCGTGTCTAACAGGTACCATGTGGGGTTCCCGCACCCAGATGAGAAGCCCCCTCCCTTCCCCGTTCACTTCCTGTTTGCAGATAGCCAGGAGTCCTTTCGTGGTTTCCACTGAGCACTGAAGGCCTGGCCGGCCTGACCACTGGGCAACCAGGCGTATCTTAAACAGCCAGTGGCCAGAGGCTGTTGGGTCATTTTCCCCACTGTCCTAGCACCGTGTCCCTGGATCTGTTTTCGTGGCTCCCTCTGGAGTCCCGACTTGCTGGGACACCGTGGCTGGGGTAGGTGCGGCTGACGGCTGTTTCCCACCCCCAG (SEQ ID NO: 11)

Cas9 guide RNAs were designed for targeting the human AAVS1 locus. A 42nucleotide RNA (referred to herein as a “crRNA” sequence) comprising (5′to 3′) a target recognition sequence (i.e., sequence complementary tothe non-coding strand of the target sequence) and protospacer sequence;a 85 nucleotide RNA (referred to herein as a “tracrRNA” sequence)comprising 5′ sequence with complementarity to the 3′ sequence of thecrRNA and additional hairpin sequence; and a chimeric RNA comprisingnucleotides 1-32 of the crRNA, a GAAA loop, and nucleotides 19-45 of thetracrRNA were prepared. The crRNA was chemically synthesized bySigma-Aldrich. The tracrRNA and chimeric RNA were synthesized by invitro transcription with T7 RNA polymerase using T7-Scribe Standard RNAIVT Kit (Cellscript). The chimeric RNA coding sequence was also placedunder the control of human U6 promoter for in vivo transcription inhuman cells. Table 4 presents the sequences of the guide RNAs.

TABLE 4 Guide RNAs SEQ ID RNA 5′-3′ Sequence NO: AAVS1-ACCCCACAGUGGGGCCACUAGUUUUAGAG 12 crRNA CUAUGCUGUUUUG tracrRNAGGAACCAUUCAAAACAGCAUAGCAAGUUA 13 AAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU chimeric ACCCCACAGUGGGGCCACUAGUUUUAGAG 14RNA CUAGAAAUAGCAAGUUAAAAUAAGGCUAG UCCG

Example 3 Preparation of Donor Polynucleotide to Monitor GenomeModification

Targeted integration of a GFP protein into the N terminus of PPP1R12Cwas used to monitor Cas9-mediated genome modification. To mediateintegration by homologous recombination a donor polynucleotide wasprepared. The AAVS1-GFP DNA donor contained a 5′ (1185 bp) AAVS1 locushomologous arm, an RNA splicing receptor, a turbo GFP coding sequence, a3′ transcription terminator, and a 3′ (1217 bp) AAVS1 locus homologousarm. Table 5 presents the sequences of the RNA splicing receptor and theGFP coding sequence followed by the 3′ transcription terminator. PlasmidDNA was prepared by using GenElute Endotoxin-Free Plasmid Maxiprep Kit(Sigma).

TABLE 5 Sequences in the AAVS1-GFP DNA donor sequence SEQ ID 5′-3′Sequence NO: RNA splicing CTGACCTCTTCTCTTCCTCCCACAG 15 receptorGFP coding GCCACCATGGACTACAAAGACGATGACGAC 16 sequence andAAGGTCGACTCTAGAGCTGCAGAGAGCGAC transcription GAGAGCGGCCTGCCCGCCATGGAGATCGAG terminator TGCCGCATCACCGGCACCCTGAACGGCGTGGAGTTCGAGCTGGTGGGCGGCGGAGAGGGC ACCCCCGAGCAGGGCCGCATGACCAACAAGATGAAGAGCACCAAAGGCGCCCTGACCTTC AGCCCCTACCTGCTGAGCCACGTGATGGGCTACGGCTTCTACCACTTCGGCACCTACCCC AGCGGCTACGAGAACCCCTTCCTGCACGCCATCAACAACGGCGGCTACACCAACACCCGC ATCGAGAAGTACGAGGACGGCGGCGTGCTGCACGTGAGCTTCAGCTACCGCTACGAGGCC GGCCGCGTGATCGGCGACTTCAAGGTGATGGGCACCGGCTTCCCCGAGGACAGCGTGATC TTCACCGACAAGATCGTCCGCAGCAACGCCACCGTGGAGCACCTGCACCCCATGGGCGAT AACGATCTGGATGGCAGCTTCACCCGCACCTTCAGCCTGCGCGACGGCGGCTACTACAGC TCCGTGGTGGACAGCCACATGCACTTCAAGAGCGCCATCCACCCCAGCATCCTGCAGAAC GGGGGCCCCATGTTCGCCTTCCGCCGCGTGGAGGAGGATCACAGCAACACCGAGCTGGGC ATCGTGGAGTACCAGCACGCCTTCAAGACCCCGGATGCAGATGCCGGTGAAGAATGAAGA TCTCTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCCCGTGCCTTCCTTGA CCCTGGAAGGTGCCACTCCCACTGTCCTTTCCTAATAAAATGAGGAAATTGCATCGCATT GTCTGAGTAGGTGTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGGGGAGG ATTGGGAAGACAATAGCAGGCATGCTGGGGATGCGGTGGGCTCTATGGACTCGAGGTTTA AACGTCGACGCGGCCGCGT

Targeted gene integration will result in a fusion protein between thefirst 107 amino acids of the PPP1R12C and the turbo GFP. The expectedfusion protein contains the first 107 amino acid residues of PPP1R12C(highlighted in grey) from RNA splicing between the first exon ofPPP1R12C and the engineered splice receptor (see Table 6).

TABLE 6 Predicted amino acid sequence of the PPP1R12C-GFP fusion protein.

LVGGGEGTPEQGRMTNKMKSTKGALTFSPYLLSHVMGYGFYHFGTYPSGYENPFLHAINNGGYTNTRIEKYEDGGVLHVSFSYRYEAGRVIGDFKVMGTGFPEDSVIFTDKIVRSNATVEHLHPMGDNDLDGSFTRTFSLRDGGYYSSVVDSHMHFKSAIHPSILQNGGPMFAFRRVEEDHSNTELGIVEYQHAFKTPDA DAGEE (SEQ ID NO: 17)

Example 4 Cas9-Mediated Targeted Integration

Transfection was performed on human K562 cells. The K562 cell line wasobtained from American Type Culture Collection (ATCC) and grown inIscove's Modified Dulbecco's Medium, supplemented with 10% FBS and 2 mML-glutamine. All media and supplements were obtained from Sigma-Aldrich.Cultures were split one day before transfection (at approximately 0.5million cells per mL before transfection). Cells were transfected withNucleofector Solution V (Lonza) on a Nucleofector (Lonza) with the T-016program. Each nucleofection contained approximately 0.6 million cells.Transfection treatments are detailed in Table 7. Cells were grown at 37°C. and 5% CO₂ immediately after nucleofection.

TABLE 7 Transfection Treatments. Treat- Donor ment Modified Cas9 GuideRNA sequence A Cas9 mRNA transcribed pre-annealed AAVS1-GFP with anAnti-Reverse Cap crRNA-tracrRNA plasmid DNA Analog (10 μg) duplex (0.3nmol) (10 μg) B Cas9 mRNA transcribed chimeric RNA AAVS1-GFP with anAnti-Reverse Cap (0.3 nmol) plasmid DNA Analog (10 μg) (10 μg) C Cas9mRNA capped via chimeric RNA AAVS1-GFP post-transcription capping (0.3nmol) plasmid DNA reaction (10 μg) (10 μg) D Cas9 plasmid DNA (10 μg)U6-chimeric AAVS1-GFP RNA plasmid plasmid DNA DNA (5 μg) (10 μg) E NoneNone AAVS1-GFP plasmid DNA (10 μg) F None None None

Fluorescence-activated cell sorting (FACS) was performed 4 days aftertransfection. FACS data are presented in FIG. 4. The percent GFPdetected in each of the four experimental treatments (A-D) was greaterthan in the control treatments (E, F), confirming integration of thedonor sequence and expression of the fusion protein.

Example 5 PCR Confirmation of Targeted Integration

Genomic DNA was extracted from transfected cells with GenElute MammalianGenomic DNA Miniprep Kit (Sigma) 12 days after transfection. Genomic DNAwas then PCR amplified with a forward primer located outside the 5′homologous arm of the AAVS1-GFP plasmid donor and a reverse primerlocated at the 5′ region of the GFP. The forward primer was5′-CCACTCTGTGCTGACCACTCT-3′ (SEQ ID NO:18) and reverse primer was5′-GCGGCACTCGATCTCCA-3′ (SEQ ID NO:19). The expected fragment size fromthe junction PCR was 1388 bp. The amplification was carried out withJumpStart Taq ReadyMix (Sigma), using the following cycling conditions:98° C. for 2 minutes for initial denaturation; 35 cycles of 98° C. for15 seconds, 62° C. for 30 seconds, and 72° C. for 1 minutes and 30seconds; and a final extension at 72° C. for 5 minutes. PCR productswere resolved on 1% agarose gel.

Cells transfected with 10 μg of Cas9 mRNA transcribed with anAnti-Reverse Cap Analog, 0.3 nmol of pre-annealed crRNA-tracrRNA duplex,and 10 μg of AAVS1-GFP plasmid DNA displayed a PCR product of theexpected size (see lane A, FIG. 5).

Example 6 Cas9-Based Genome Editing in Mouse Embryos

The mouse Rosa26 locus can be targeted for genome modifications. Table 8presents a portion of the mouse Rosa26 sequence in which potentialtarget sites are shown in bold. Each target site comprises aprotospacer.

TABLE 8 Mouse Rosa26 SequenceGAGCGGCTGCGGGGCGGGTGCAAGCACGTTTCCGACTTGAGTTGCCTCAAGAGGGGCGTGCTGAGCCAGACCTCCATCGCGCACTCCGGGGAGTGGAGGGAAGGAGCGAGGGCTCAGTTGGGCTGTTTTGGAGGCAGGAAGCACTTGCTCTCCCAAAGTCGCTCTGAGTTGTTATCAGTAAGGGAGCTGCAGTGGAGTAGGCGGGGAGAAGGCCGCACCCTTCTCCGGAGGGGGGAGGGGAGTGTTGCAATACCTTTCTGGGAGTTCTCTGCTGCCTCCTGGCTTCTGAGGACCGCCCTGGGCCTGGGAGAATCCCTTCCCCCTCTTCCCTCGTGATCTGCAACTCCAGTCTTTCTAGAAGATGGGCGGGAGTCTTCTGGGCAGGCTTAAAGGCTAACCTGGTGTGTGGGCGTTGTCCTGCAGGGGAATTGAACAGGTGTAAAATTGGAGGGACAAGACTTCCCACAGATTTTCGGTTTTGTCGGGAAGTTTTTTAATAGGGGCAAATAAGGAAAATGGGAGGATAGGTAGTCATCTGGGGTTTTATGCAGCAAAACTACAGGTTATTATTGCTTGTGATCCGCCTCGGAGTATTTTCCATCGAGGTAGATTAAAGACATGCTCACCCGAGTTTTATACTCTCCTGCTTGAGATCCTTACTACAGTATGAAATTACAGTGTCGCGAGTTAGACTATGTAAGCAGAATTTTA (SEQ ID NO: 20)

Guide RNAs were designed to target each of the target sites in the mouseRosa26 locus. The sequences are shown in Table 9, each is 42 nucleotidesin length and the 5′ region is complementary to the strand that is notpresented in Table 8 (i.e., the strand that is complementary to thestrand shown in Table 8).

TABLE 9 Mouse Rosa26 Guide RNAs SEQ ID RNA 5′-3′ Sequence NO: mRosa26-CUCCAGUCUUUCUAGAAGAUGUUUUAGAGCUAU 21 crRNA-1 GCUGUUUUG mRosa26-UGAACAGGUGUAAAAUUGGAGUUUUAGAGCUAU 22 crRNA-2 GCUGUUUUG mRosa26-UGUCGGGAAGUUUUUUAAUAGUUUUAGAGCUAU 23 crRNA-3 GCUGUUUUG

The crRNAs were chemically synthesized and pre-annealed to the tracrRNA(SEQ ID NO:13; see Example 2). Pre-annealed crRNA/tracrRNA and in vitrotranscribed mRNA encoding modified Cas9 protein (SEQ ID NO. 9; seeExample 1) can be microinjected into the pronuclei of fertilized mouseembryos. Upon guidance to the target set by the crRNA, the Cas9 proteincleaves the target site, and the resultant double-stranded break can berepaired via a non-homologous end-joining (NHEJ) repair process. Theinjected embryos can be either incubated at 37° C., 5% CO₂ overnight orfor up to 4 days, followed by genotyping analysis, or the injectedembryos can be implanted into recipient female mice such that live bornanimals can be genotyped. The in vitro-incubated embryos or tissues fromlive born animals can be screened for the presence of Cas9-inducedmutation at the Rosa locus using standard methods. For example, theembryos or tissues from fetus or live-born animals can be harvested forDNA extraction and analysis. DNA can be isolated using standardprocedures. The targeted region of the Rosa26 locus can be PCR amplifiedusing appropriate primers. Because NHEJ is error-prone, deletions of atleast one nucleotide, insertions of at least one nucleotide,substitutions of at least one nucleotide, or combinations thereof canoccur during the repair of the break. Mutations can be detected usingPCR-based genotyping methods, such as Cel-I mismatch assays and DNAsequencing.

Example 7 Cas9-Based Genome Modification in Mouse Embryos

The Rosa26 locus can be modified in mouse embryos by co-injecting adonor polynucleotide, as detailed above in section (IV)(d), along withthe pre-annealed crRNA/tracrRNA and mRNA encoding modified Cas9 asdescribed above in Example 6. In vitro-incubated embryos or tissues fromlive born animals (as described in Example 6) can be screened for amodified Rosa26 locus using PCR-based genotyping methods, such as RFLPassays, junction PCR, and DNA sequencing.

Example 8 Cas9-Based Genome Editing in Rat Embryos

The rat Rosa26 locus can be targeted for genome modifications. Table 10presents a portion of the rat sequence in which potential target sitesare shown in bold. Each target site comprises a protospacer.

TABLE 10 Rat Rosa26 SequenceGGGATTCCTCCTTGAGTTGTGGCACTGAGGAACGTGCTGAACAAGACCTACATTGCACTCCAGGGAGTGGATGAAGGAGTTGGGGCTCAGTCGGGTTGTATTGGAGACAAGAAGCACTTGCTCTCCAAAAGTCGGTTTGAGTTATCATTAAGGGAGCTGCAGTGGAGTAGGCGGAGAAAAGGCCGCACCCTTCTCAGGACGGGGGAGGGGAGTGTTGCAATACCTTTCTGGGAGTTCTCTGCTGCCTCCTGTCTTCTGAGGACCGCCCTGGGCCTGGAAGATTCCCTTCCCCCTTCTTCCCTCGTGATCTGCAACTGGAGTCTTTCTGGAAGATAGGCGGGAGTCTTCTGGGCAGGCTTAAAGGCTAACCTGGTGCGTGGGGCGTTGTCCTGCAGAGGAATTGAACAGGTGTAAAATTGGAGGGGCAAGACTTCCCACAGATTTTCGATTGTGTTGTTAAGTATTGTAATAGGGGCAAATAAGGGAAATAGACTAGGCACTCACCTGGGGTTTTATGCAGCAAAACTACAGGTTATTATTGCTTGTGATCCGCCCTGGAGAATTTTTCACCGAGGTAGATTGAAGACATGCCCACCCAAATTTTAATATTCTTCCACTTGCGATCCTTGCTACAGTA TGAAA (SEQ ID NO: 24)

Guide RNAs were designed to target each of the target sites in the ratRosa26 locus. The sequences are shown in Table 11, each is 42nucleotides in length and the 5′ region is complementary to the strandthat is not presented in Table 10 (i.e., the strand that iscomplementary to the strand shown in Table 10).

TABLE 11 Rat Rosa26 Guide RNAs SEQ ID RNA 5′-3′ Sequence NO: rRosa26-AGGGGGAAGGGAAUCUUCCAGUUUUAGAGCUA 25 crRNA-1 UGCUGUUUUG rRosa26-UCUGCAACUGGAGUCUUUCUGUUUUAGAGCUA 26 crRNA-2 UGCUGUUUUG rRosa26-AGGCGGGAGUCUUCUGGGCAGUUUUAGAGCUA 27 crRNA-3 UGCUGUUUUG

The crRNAs were chemically synthesized and pre-annealed to the tracrRNA(SEQ ID NO:13; see Example 2). Pre-annealed crRNA/tracrRNA and in vitrotranscribed mRNA encoding modified Cas9 protein (SEQ ID NO. 9; seeExample 1) can be microinjected into the pronuclei of fertilized ratembryos. Upon guidance to the target site by the crRNA, the Cas9 proteincleaves the target site, and the resultant double-stranded break can berepaired via a non-homologous end-joining (NHEJ) repair process. Theinjected embryos can be either incubated at 37° C., 5% CO₂ overnight orfor up to 4 days, followed by genotyping analysis, or the injectedembryos can be implanted into recipient female mice such that live bornanimals can be genotyped. The in vitro-incubated embryos or tissues fromlive born animals can be screened for the presence of Cas9-inducedmutation at the Rosa locus using standard methods. For example, theembryos or tissues from fetus or live-born animals can be harvested forDNA extraction and analysis. DNA can be isolated using standardprocedures. The targeted region of the Rosa26 locus can be PCR amplifiedusing appropriate primers. Because NHEJ is error-prone, deletions of atleast one nucleotide, insertions of at least one nucleotide,substitutions of at least one nucleotide, or combinations thereof canoccur during the repair of the break. Mutations can be detected usingPCR-based genotyping methods, such as Cel-I mismatch assays and DNAsequencing.

Example 9 Cas9-Based Genome Modification in Rat Embryos

The Rosa26 locus can be modified in rat embryos by co-injecting a donorpolynucleotide, as detailed above in section (IV)(d), along with thepre-annealed crRNA/tracrRNA and mRNA encoding modified Cas9 as describedabove in Example 8. In vitro-incubated embryos or tissues from live bornrats (as described in Example 8) can be screened for a modified Rosa26locus using PCR-based genotyping methods, such as RFLP assays, junctionPCR, and DNA sequencing.

1-12. (canceled)
 13. A method for modifying a chromosomal sequence in aeukaryotic cell or embryo, the method comprising: a) introducing intothe eukaryotic cell or embryo (i) at least one RNA-guided endonucleasecomprising at least one nuclear localization signal or nucleic acidencoding at least one RNA-guided endonuclease comprising at least onenuclear localization signal, (ii) at least one guide RNA or DNA encodingat least one guide RNA, and, optionally, (iii) at least one donorpolynucleotide; and b) culturing the eukaryotic cell or embryo such thateach guide RNA directs an RNA-guided endonuclease to a targeted site inthe chromosomal sequence where the RNA-guided endonuclease introduces adouble-stranded break in the targeted site, and the double-strandedbreak is repaired by a DNA repair process such that the chromosomalsequence is modified.
 14. The method of claim 13, wherein the RNA-guidedendonuclease is derived from a Cas9 protein.
 15. The method of claim 13,wherein the nucleic acid encoding the RNA-guided endonuclease is mRNA.16. The method of claim 13, wherein the nucleic acid encoding theRNA-guided endonuclease is DNA.
 17. The method of claim 16, wherein theDNA is part of a vector that further comprises a sequence encoding theguide RNA.
 18. The method of claim 13, wherein the eukaryotic cell is ahuman cell, a non-human mammalian cell, a stem cell, a non-mammalianvertebrate cell, an invertebrate cell, a plant cell, or a single celleukaryotic organism.
 19. The method of claim 13, wherein the embryo is anon-human one cell animal embryo.
 20. A fusion protein comprising aCRISPR/Cas-like protein or fragment thereof and an effector domain. 21.The fusion protein of claim 20, wherein the CRISPR/Cas-like protein isderived from a Cas9 protein.
 22. The fusion protein of claim 21, whereinthe Cas9 protein is modified to lack at least one functional nucleasedomain.
 23. The fusion protein of claim 21, wherein the Cas9 protein ismodified to lack all nuclease activity. 24-28. (canceled)
 29. The fusionprotein of claim 20, wherein the effector domain is chosen from atranscriptional activation domain, a transcriptional repressor domain,and an epigenetic modification domain.
 30. The fusion protein of claim20, wherein the fusion protein further comprises at least one additionaldomain chosen from a nuclear localization signal, a cell-penetratingdomain, and a marker domain.
 31. (canceled)
 32. A method for modifying achromosomal sequence or regulating expression of a chromosomal sequencein a cell or embryo, the method comprising introducing into the cell orembryo (a) at least one fusion protein or nucleic acid encoding at leastone fusion protein, wherein the fusion protein comprises aCRISPR/Cas-like protein or a fragment thereof and an effector domain,and (b) at least one guide RNA or DNA encoding at least one guide RNA,wherein the one guide RNA guides the CRISPR/Cas-like protein of thefusion protein to a targeted site in the chromosomal sequence and theeffector domain of the fusion protein modifies the chromosomal sequenceor regulates expression of the chromosomal sequence.
 33. The method ofclaim 32, wherein the CRISPR/Cas-like protein is derived from a Cas9protein.
 34. The method of claim 33, wherein the cas9 protein ismodified to lack at least one functional nuclease domain.
 35. The methodof claim 33, wherein the cas9 protein is modified to lack all nucleaseactivity.
 36. The method of claim 32, wherein fusion protein furthercomprises at least one additional domain chosen from a nuclearlocalization signal, a cell-penetrating domain, and a marker domain. 37.(canceled)
 38. The method of claim 32, wherein one fusion protein ornucleic acid encoding one fusion protein and two guide RNAs or DNAencoding two guide RNAs are introduced into the cell or embryo.
 39. Themethod of claim 38, wherein the fusion protein comprises a Cas9 proteinor fragment thereof.
 40. The method of claim 32, wherein two fusionproteins or nucleic acid encoding two fusion proteins and two guide RNAsor DNA encoding two guide RNAs are introduced into the cell or embryo.41. The method of claim 40, wherein each fusion protein comprises adifferent Cas9 protein or fragment thereof. 42-43. (canceled)
 44. Themethod of claim 32, further comprising introducing into the cell orembryo at least one donor polynucleotide.
 45. The method of claim 32,wherein the effector domain is chosen from an epigenetic modificationdomain, a transcriptional activation domain, or a transcriptionalrepressor domain.
 46. The method of claim 45, wherein one fusion proteinor nucleic acid encoding one fusion protein, and one guide RNA or DNAencoding one guide RNA are introduced into the cell or embryo.
 47. Themethod of claim 32, wherein the cell is a human cell, a non-humanmammalian cell, a stem cell, a non-mammalian vertebrate cell, aninvertebrate cell, a plant cell, or a single cell eukaryotic organism.48. The method of claim 32, wherein the embryo is a non-human one cellanimal embryo.